Translocations are a tool widely used by wildlife managers, yet their impact is often insufficiently evaluated. Most translocation studies only assess the initial establishment phase, and the ...majority of long-term persistence studies to date have only tracked female fecundity. Male genetic integration for mitigative translocations have as of yet not been assessed and could greatly undermine the validity of translocation evaluations. To test for successful male integration, we determined genetic paternity of 92 desert tortoise hatchlings (Gopherus agassizii), from both resident and translocated females, four years after the initial translocation event and found that all 35 hatchlings with a paternal match in our genotype database were sired by residents. Given that translocated males constitute 46% of the genotyped males found in the home ranges of the females, they produce significantly fewer offspring than resident males in the same area (G-test, p value <0.0001). This is the first study assessing paternal genetic integration following a translocation of a wild sourced population into a native resident population. We hypothesize that male condition following the translocation, female mate preference for prior residents and competitive exclusion by resident males may contribute to the lower reproductive output of translocated males. We advocate the use of genetic paternity testing in other species to determine the generality of male translocation success across taxa given this unexpected and alarming result.
•Fecundity levels for translocated male tortoises are significantly lower than resident male tortoises.•This difference is not found for females.•Female appear to prefer resident males by either pre- or post zygotic mate choice.•This pattern is observed for both resident as well translocated females.•Parentage analysis should be included in other translocation studies.
FMS-related tyrosine kinase 3 ligand (FLT3L), encoded by FLT3LG, is a hematopoietic factor essential for the development of natural killer (NK) cells, B cells, and dendritic cells (DCs) in mice. We ...describe three humans homozygous for a loss-of-function FLT3LG variant with a history of various recurrent infections, including severe cutaneous warts. The patients’ bone marrow (BM) was hypoplastic, with low levels of hematopoietic progenitors, particularly myeloid and B cell precursors. Counts of B cells, monocytes, and DCs were low in the patients’ blood, whereas the other blood subsets, including NK cells, were affected only moderately, if at all. The patients had normal counts of Langerhans cells (LCs) and dermal macrophages in the skin but lacked dermal DCs. Thus, FLT3L is required for B cell and DC development in mice and humans. However, unlike its murine counterpart, human FLT3L is required for the development of monocytes but not NK cells.
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•Human FLT3L deficiency underlies bone-marrow failure and infectious diseases•Human and mouse FLT3L deficiencies impair dendritic and B cell development•FLT3L deficiency impairs monocyte development in humans but not mice•FLT3L deficiency impairs NK cell development in mice but not in humans
Adult humans with inherited, complete FLT3L deficiency enable valuable insights into the role of the hematopoietic growth factor FLT3L in human hematopoiesis, revealing that FLT3L deficiencies impair monocyte, dendritic, and B cell development but not NK cell development. This study reveals key differences in the role of FLT3L in humans versus mice.
Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across ...studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance.
Understanding how species adapt to their local environment is a central question in evolutionary biology. Natural selection acts on the phenotypic level, but it is the corresponding genotype that is ...passed onto the next generation and can become fixed in populations and species over time. Characterizing the genetic basis of phenotypic traits is thus a crucial step in the study of adaptation that has recently become more attainable due to advances in the field of genomics. Newly developed genomic tools can generate population-level markers across the genome to study variation within and among species, directly linking genetic polymorphisms with the observed phenotypic traits of interest. These tools have, however, not been widely applied to amphibians due to their exceptionally large genomes, and associated challenges with regards to sequencing, assembly and genotyping.This thesis attempts to improve our understanding of amphibian genomics and the study of local adaptation by applying and optimizing genomic tools in two amphibian systems that show intraspecific variation in adaptive traits. The fire salamander, Salamandra salamandra, exhibits two viviparous reproductive modes: larviparity, in which females deliver larvae into nearby waterbodies, and pueriparity, with females delivering fully developed juveniles. This adaptive trait allows salamanders to reproduce in environments lacking water bodies, opening up new habitats with profound ecological and evolutionary implications. The lowland leopard frog (Rana yavapaiensis) displays variation in disease susceptibility, with resistance to the fungal disease chytridiomycosis differing widely been individuals and populations and driving adaptation in a disease dominated environment. Both S. salamandra and R. yavapaiensis have large genomes (~35 Gb and ~6 Gb respectively), show intraspecific variation in adaptive traits and are well studied at different biological levels, but adaptive traits have never been investigated using genomic tools. The two systems are thus prime natural laboratories to assess and optimize the usage of genomic tools on questions of local adaptation in large amphibian genomes. Following a general introduction on concepts and techniques in the study of adaptation, I summarize the current state of the art on amphibian genomics and report on the challenges posed by large genomes, and discuss some of the potential solutions. By using techniques such as RNA-seq and exome capture with associated bioinformatic analyses, we can focus on the coding regions of the genome and measure functional genetic variation across genomic space. We can subsequently use these markers to reconstruct the evolutionary history and relationships between populations, characterize gene expression differences between adaptive phenotypes, and identify candidate genes associated with our traits of interest.To assess the effectiveness of exome capture for ancestral state reconstruction, I reconstructed a phylogeny of the Salamandra genus using genome-wide markers and direct observations of births to identify the geographic and phylogenetic extent of larviparity and pueriparity in Salamandra. I focused on the clades and regions that display differences in reproductive mode to detect the number and timing of transitions between reproductive modes. I identified five independent transitions from larviparity to pueriparity occurring at different evolutionary timescales ranging from the Pliocene to the Pleistocene. Three of these transitions occurred within S. salamandra providing multiple convergent instances of intraspecific variation in reproductive mode that can help control for evolutionary history and identify the genetic basis of reproductive mode shifts.
The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. ...Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class 11β chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.
The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and "disease resistance. ...Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class II beta chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.
Abstract
Biodiversity loss is extreme in amphibians. Despite ongoing conservation action, it is difficult to determine where we stand in overcoming their extinction crisis. Among the most threatened ...amphibians are the 131 Neotropical harlequin toads. Many of them declined since the 1980s with several considered possibly extinct. Recently, more than 30 species have been rediscovered, raising hope for a reversing trend in the amphibian extinction crisis. We use past and present data available for harlequin toads (
Atelopus
), to examine whether the amphibian extinction crisis is still in an emergency state. Since 2004 no species has improved its population status, suggesting that recovery efforts have not been successful. Threats include habitat change, pathogen spread and climate change. More mitigation strategies need implementation, especially habitat protection and disease management, combined with captive conservation breeding. With harlequin toads serving as a model, it is clear that the amphibian extinction crisis is still underway.
