The influence of habitat quality on demography, dispersal and population structure of great crested newts (Triturus cristatus)

The great crested newt (Triturus cristatus) is an amphibian species of European conservation concern that has suffered severe declines, primarily due to habitat loss and fragmentation. This pond-breeding amphibian lives in spatially structured populations (SSPs) where dispersal strongly influences population dynamics, genetics and thereby the long-term persistence of the whole SSP. This dissertation investigates the effects of habitat quality on demography and how such environmental as well as individual factors influence different stages of the dispersal process and consequently the population structure of great crested newts. The evaluation of a commonly used habitat suitability index (HSI) model showed no relationship between habitat quality and individual survival probability or body condition but a positive association with reproduction probability and abundance, making it a useful tool to identify habitats of higher priority for species conservation. A comprehensive analysis of dispersal and population structure combining extensive demographic and genetic data highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in a patchy population of great crested newts. Finally, the monitoring of 18 newly created ponds revealed that ponds were rapidly colonized, mostly over short distances, and that newts captured in new ponds were younger and tended to be larger than those in established ponds (phenotype-dependent dispersal), indicating that colonization is predominantly the result of natal dispersal by large individuals. Implications for conservation management are being discussed including corresponding recommendations.:Zusammenfassung..........1 Summary..........7 Introduction..........12 Chapter I (Linking habitat suitability to demography in a pond-breeding amphibian)..........24 Chapter II (The relationship between habitat suitability, population size and body condition in a pond-breeding amphibian)..........38 Chapter III (Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population)..........50 Chapter IV (Pond construction for amphibian conservation: phenotypic traits influence the colonization process)..........99 Acknowledgements..........127 Author contributions..........12

Context‐dependent dispersal determines relatedness and genetic structure in a patchy amphibian population

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across a SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.Microsatellite Genotypes: Missing values are coded "-9". Presence/Absence Data: Missing values are coded "-". Funding provided by: Deutsche ForschungsgemeinschaftCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659Award Number: STE 1130/7-1Demographic Data (CMR and Presence/Absence Data): We surveyed 33 water bodies using mark-recapture methods for the presence, demography and reproduction of crested newts between 2012 and 2014. Newts were captured during two capture sessions (cs) per year, one early (April/May) and one late (June/July) in the breeding season. Every capture session thereby consisted of three consecutive capture events in intervals of two days. Within the context of a presence/absence analysis, all sites were surveyed for one more day in late July/early August in order to detect larvae. If a pond dried out and was therefore not surveyed during a capture session, such an event was treated as a missing observation. Newts were captured using Ortmann's funnel traps which were evenly distributed along the shoreline of a pond. The number of traps deployed per capture event varied according to pond perimeter (one trap per 10m shoreline), ranging from one to 27 traps. For individual recognition of newts during the CMR study, we used photographs of the ventral side of an individual which provides a natural marking in form of a highly variable but individually unique and stable color pattern through the time. Recaptured individuals were identified automatically by the software AmphIdent. Microsatellite Genotypes: Tissue samples were taken from seven sampling sites by puncturing the tails of captured great crested newts (Triturus cristatus) using micro haematocrit capillary tubes (Carl Roth, Ø 1.6 mm) and were then stored in 80% ethanol. Total genomic DNA was extracted using the sodium dodecyl sulfate (SDS)-proteinase K/ Phenol-Chloroform extraction method. Genomic DNA was stored in Tris-EDTA buffer (10 mM Tris-HCl, 0.1 mM EDTA, pH 8.0) and used for all subsequent reactions. Each individual sample was mugenotyped for 17 microsatellite loci. Primers were combined in three multiplex mixes (Drechsler et al., 2013). 10 µl Type-it Multiplex PCRs (Qiagen) containing 1 µl of genomic DNA were performed. The PCR profile was as follows: (1) 5 min at 95°C, (2) 30 s at 94°C, (3) 90 s at an annealing temperature of 60°C, (4) 60 s at 72°C, (5) return to step 2 for 30 times, (6) 30 min at 60°C. Obtained PCR products were diluted with 50-200 μl water depending on the strength of obtained PCR products. 1 µl of each diluted multiplex reaction was added to 20 μl of Genescan 500-LIZ size standard (Applied Biosystem) and then run on an ABI 3730 96-capillary or an ABI 3130 16-capillary automated DNA-sequencer. Allele scoring of microsatellite loci was performed using Genemarker software (SoftGenetics version 1.95)

The influence of habitat quality on demography, dispersal and population structure of great crested newts (Triturus cristatus)

The great crested newt (Triturus cristatus) is an amphibian species of European conservation concern that has suffered severe declines, primarily due to habitat loss and fragmentation. This pond-breeding amphibian lives in spatially structured populations (SSPs) where dispersal strongly influences population dynamics, genetics and thereby the long-term persistence of the whole SSP. This dissertation investigates the effects of habitat quality on demography and how such environmental as well as individual factors influence different stages of the dispersal process and consequently the population structure of great crested newts. The evaluation of a commonly used habitat suitability index (HSI) model showed no relationship between habitat quality and individual survival probability or body condition but a positive association with reproduction probability and abundance, making it a useful tool to identify habitats of higher priority for species conservation. A comprehensive analysis of dispersal and population structure combining extensive demographic and genetic data highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in a patchy population of great crested newts. Finally, the monitoring of 18 newly created ponds revealed that ponds were rapidly colonized, mostly over short distances, and that newts captured in new ponds were younger and tended to be larger than those in established ponds (phenotype-dependent dispersal), indicating that colonization is predominantly the result of natal dispersal by large individuals. Implications for conservation management are being discussed including corresponding recommendations.:Zusammenfassung..........1 Summary..........7 Introduction..........12 Chapter I (Linking habitat suitability to demography in a pond-breeding amphibian)..........24 Chapter II (The relationship between habitat suitability, population size and body condition in a pond-breeding amphibian)..........38 Chapter III (Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population)..........50 Chapter IV (Pond construction for amphibian conservation: phenotypic traits influence the colonization process)..........99 Acknowledgements..........127 Author contributions..........12

The influence of habitat quality on demography, dispersal and population structure of great crested newts (Triturus cristatus)

The great crested newt (Triturus cristatus) is an amphibian species of European conservation concern that has suffered severe declines, primarily due to habitat loss and fragmentation. This pond-breeding amphibian lives in spatially structured populations (SSPs) where dispersal strongly influences population dynamics, genetics and thereby the long-term persistence of the whole SSP. This dissertation investigates the effects of habitat quality on demography and how such environmental as well as individual factors influence different stages of the dispersal process and consequently the population structure of great crested newts. The evaluation of a commonly used habitat suitability index (HSI) model showed no relationship between habitat quality and individual survival probability or body condition but a positive association with reproduction probability and abundance, making it a useful tool to identify habitats of higher priority for species conservation. A comprehensive analysis of dispersal and population structure combining extensive demographic and genetic data highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in a patchy population of great crested newts. Finally, the monitoring of 18 newly created ponds revealed that ponds were rapidly colonized, mostly over short distances, and that newts captured in new ponds were younger and tended to be larger than those in established ponds (phenotype-dependent dispersal), indicating that colonization is predominantly the result of natal dispersal by large individuals. Implications for conservation management are being discussed including corresponding recommendations.:Zusammenfassung..........1 Summary..........7 Introduction..........12 Chapter I (Linking habitat suitability to demography in a pond-breeding amphibian)..........24 Chapter II (The relationship between habitat suitability, population size and body condition in a pond-breeding amphibian)..........38 Chapter III (Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population)..........50 Chapter IV (Pond construction for amphibian conservation: phenotypic traits influence the colonization process)..........99 Acknowledgements..........127 Author contributions..........12

Context‐dependent dispersal determines relatedness and genetic structure in a patchy amphibian population

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance and direction, these individual-level decisions further modulate the demography, relatedness and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a great crested newt (Triturus cristatus) SSP. We collected capture–recapture data of 5564 individuals and genetic data of 950 individuals across an SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes

Hunted hunters? Effect of group size on predation risk and growth in the Australian subsocial crab spider Diaea ergandros

A reduced predation risk is considered to be a major adaptive advantage of sociality. While most studies are concerned with non-predatory prey species, group-living predators are likely to face similar threats from higher-order predators. We studied the relationship between group size and predation risk in the subsocial crab spider Diaea ergandros by testing predictions from theoretical models including attack abatement as well as the formation of protective retreats. In a field survey, we found predatory clubionid spiders in 35 % of the D. ergandros nests and as predicted, nest size did not correlate with predator presence. In a subsequent laboratory experiment, we observed survival probability, nest construction activity and feeding behaviour including weight development between groups of different sizes as well as in the absence or presence of a predator. Large groups had an advantage in terms of survival and growth compared to smaller groups or single individuals. They also built significantly larger nests than smaller groups, supporting the idea of protective retreat formation being an adaptive benefit to group living. Even though clubionids did attack D. ergandros, they did not significantly affect overall mortality of D. ergandros. The feeding experiment showed that spiders fed on a larger proportion of flies in the presence of a predator. However, these groups gained significantly less weight compared to the control groups, indicating that the potential predators not only act as predators but also as food competitors, constituting a twofold cost for D. ergandros.10 page(s

The relationships between habitat suitability, population size and body condition in a pond-breeding amphibian

The ecological niche of a species determines whether a species can persist and reproduce in a patch or not. The niche of a species is often described using habitat suitability models and indices. Accordingly, one may expect tight links between demography, phenotypes of individuals, population size, and habitat suitability. However, such links are not always found. Here, we study the relationship between a habitat suitability index that is commonly used for conservation assessments and metrics describing the performance at the level of populations and individuals. Using data from a metapopulation of a pond-breeding amphibian, the Great Crested Newt (Triturus cristatus), we show that habitat suitability predicts population size but not body condition. Ponds with higher suitability had a higher population size of newts, whereas population size correlated negatively with body condition of individuals. Our results are in line with previous studies showing no straightforward relationship between habitat suitability and body condition (a measure of individual performance) and the performance of populations. We suggest that a population size-dependent reduction of body condition may be a regulatory mechanism in newt populations

Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria.

Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bioproducts, we developed a versatile platform for the construction of broad-host-range vector systems. This platform includes the following features: (i) an efficient assembly strategy in which modules released from 3 to 4 donor plasmids or produced by polymerase chain reaction are assembled by isothermal assembly guided by short GC-rich overlap sequences. (ii) A growing library of molecular devices categorized in three major groups: (a) replication and chromosomal integration; (b) antibiotic resistance; (c) functional modules. These modules can be assembled in different combinations to construct a variety of autonomously replicating plasmids and suicide plasmids for gene knockout and knockin. (iii) A web service, the CYANO-VECTOR assembly portal, which was built to organize the various modules, facilitate the in silico construction of plasmids, and encourage the use of this system. This work also resulted in the construction of an improved broad-host-range replicon derived from RSF1010, which replicates in several phylogenetically distinct strains including a new experimental model strain Synechocystis sp. WHSyn, and the characterization of nine antibiotic cassettes, four reporter genes, four promoters, and a ribozyme-based insulator in several diverse cyanobacterial strains

Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria.

Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bioproducts, we developed a versatile platform for the construction of broad-host-range vector systems. This platform includes the following features: (i) an efficient assembly strategy in which modules released from 3 to 4 donor plasmids or produced by polymerase chain reaction are assembled by isothermal assembly guided by short GC-rich overlap sequences. (ii) A growing library of molecular devices categorized in three major groups: (a) replication and chromosomal integration; (b) antibiotic resistance; (c) functional modules. These modules can be assembled in different combinations to construct a variety of autonomously replicating plasmids and suicide plasmids for gene knockout and knockin. (iii) A web service, the CYANO-VECTOR assembly portal, which was built to organize the various modules, facilitate the in silico construction of plasmids, and encourage the use of this system. This work also resulted in the construction of an improved broad-host-range replicon derived from RSF1010, which replicates in several phylogenetically distinct strains including a new experimental model strain Synechocystis sp. WHSyn, and the characterization of nine antibiotic cassettes, four reporter genes, four promoters, and a ribozyme-based insulator in several diverse cyanobacterial strains