Data from: Phenotype-associated inbreeding biases estimates of inbreeding depression in a wild bird population
Contributors: Becker, Philipp J. J., Hegelbach, Johann, Keller, Lukas F., Postma, Erik
... Inbreeding depression is usually quantified by regressing individual phenotypic values on inbreeding coefficients, implicitly assuming there is no correlation between an individual's phenotype and the kinship coefficient to its mate. If such an association between parental phenotype and parental kinship exists, and if the trait of interest is heritable, estimates of inbreeding depression can be biased. Here we first derive the expected bias as a function of the covariance between mean parental breeding value and parental kinship. Subsequently, we use simulated data to confirm the existence of this bias, and show that it can be accounted for in a quantitative genetic animal model. Finally, we use long-term individual-based data for white-throated dippers (Cinclus cinclus), a bird species in which inbreeding is relatively common, to obtain empirical estimate of this bias. We show that during part of the study period, parents of inbred birds had shorter wings than those of outbred birds, and as wing length is heritable, inbred individuals were smaller, independent of any inbreeding effects. This resulted in the overestimation of inbreeding effects. Similarly, during a period when parents of inbred birds had longer wings, we found that inbreeding effects were underestimated. We discuss how such associations may have arisen in this system, and why they are likely to occur in others, too. Overall, we demonstrate how less biased estimates of inbreeding depression can be obtained within a quantitative genetic framework, and suggest that inbreeding and additive genetic effects should be accounted for simultaneously whenever possible.
Data from: Molecular and morphological perspectives on the circumscription of Carex section Heleoglochin (Cyperaceae)
Contributors: Molina, Ana, Chung, Kyong-Sook, Hipp, Andrew L.
... Vignea is the only monophyletic subgenus in the genus Carex (Cyperaceae), comprising nearly 300 members grouped into 19–28 sections. Molecular studies have demonstrated that most of these sections are polyphyletic. Here, we seek to clarify the relationships among species in section Heleoglochin based on phylogenetic and morphological analyses. We analyzed sequence data using nuclear ribosomal DNA internal and external transcriber spacer regions of 60 representative specimens of sect. Heleoglochin, representing the full geographic range of the section and of species that are themselves geographically widespread. We used maximum likelihood and Bayesian inference to estimate phylogeny and divergence times based on molecular data. We scored 17 vegetative and inflorescence characters on 303 specimens and 23 perigynium characters on 56 specimens to characterize morphological variation within and among species and clades. We undertook a comparative analysis of morphological, molecular, and biogeographic patterns to evaluate sectional limits and relationships. Our findings confirm that section Heleoglochin is polyphyletic, with three main lineages—Eurasiatic, North American, and Oceanic clades—supported by molecular, morphological, and biogeographic data. Morphological and molecular analyses support two disjunctures: the European species Carex appropinquata appears sister to the Oceanic lineage, and all the specimens of C. diandra distributed worldwide are grouped together in the North American clade. Concordance among morphological, molecular, and biogeographic data supports each of the lineages and highlights the potential of integrative studies to illuminate the causes of mismatches between phylogeny and traditional classifications. Such integrative studies are needed to make headway on the systematics of this thorny genus, in which non-monophyly of traditional sections is the rule rather than the exception.
Data from: Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.
Contributors: Ingram, Colleen M., Troendle, Nicholas J., Gill, Clare A., Braude, Stanton, Honeycutt, Rodney L.
... The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as a mating system) are the driving forces for the evolution of this eusocial species. One caveat to accepting this long-held view is that the original genetic studies were based on limited sampling from the species’ geographic distribution. A growing body of evidence supports a contrary view, with the original samples not representative of the species—rather reflecting a single founder event, establishing a small population south of the Athi River. Our study is the first to address these competing hypotheses by examining patterns of molecular variation in colonies sampled from north and south of the Athi and Tana rivers, which based on our results, serve to isolate genetically distinct populations of naked mole-rats. Although colonies south of the Athi River share a single mtDNA haplotype and are fixed at most microsatellite loci, populations north of the Athi River are considerably more variable. Our findings support the position that the low variation observed in naked mole-rat populations south of the Athi River reflects a founder event, rather than a consequence of this species’ unusual mating system.
Data from: Oceanographic currents and local ecological knowledge indicate, and genetics does not refute, a contemporary pattern of larval dispersal for the ornate spiny lobster, Panulirus ornatus in the South-East Asian archipelago
Contributors: Dao, Hoc Tan, Smith-Keune, Carolyn, Wolanski, Eric, Jones, Clive M., Jerry, Dean R.
... Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.
Data from: The impact of HCV infection duration on HIV disease progression and response to cART amongst HIV seroconverters in the UK
Contributors: Inshaw, Jamie, Leen, Clifford, Fisher, Martin, Gilson, Richard, Hawkins, David, Collins, Simon, Fox, Julie, McLean, Ken, Fidler, Sarah, Phillips, Andrew
... Introduction: The effect of HCV infection on HIV disease progression remains unclear; the effect of HCV infection duration on HIV disease progression is unknown. Methods: We used data from a cohort of HIV seroconverters to investigate the effect of HCV infection duration on time from HIV seroconversion to CD4 4 years). We additionally compared CD4 cell decline following HCV infection to that of mono-infected individuals with similar HIV infection duration by fitting a random effects model. In a separate analysis, we used linear mixed models to we examine the effect of HCV infection and its duration on CD4 increase over 48 weeks following cART. Results: Of 1655 individuals, 97 (5.9%) were HCV co-infected. HCV4 years respectively), compared to mono-infected individuals. However, we found no evidence of an association for those with HCV>2 years (all p>0.89). Individuals experienced a somewhat greater decrease in CD4 count following HCV infection lasting 13 months, relative to individuals with HIV alone, (estimate = -3.33, 95% CI [-7.29, 0.63] cells/mm3 per month, p = 0.099). Of 1502 initiating cART, 106 (7.1%) were HCV co-infected, with no evidence of HCV duration at cART being associated with immunological response (p = 0.45). Conclusions: The impact of HCV co-infection on HIV disease progression appears to be restricted to the first year after HCV infection.
Contributors: Rawlence, Nicolas J., Kennedy, Martyn, Anderson, Christian N. K., Prost, Stefan, Till, Charlotte E., Smith, Ian, Scofield, R. Paul, Tennyson, Alan J. D., Hamel, Jill, Lalas, Chris
... Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines.
Data from: Identification of the Minimal Cytolytic Unit for Streptolysin S and an Expansion of the Toxin Family
Contributors: Molloy, Evelyn M., Casajens, Sherwood R., Cox, Courtney L., Maxson, Tucker, Ethridge, Nicole A., Margos, Gabriele, Fingerle, Volker, Mitchell, Douglas A.
... Background: Streptolysin S (SLS) is a cytolytic virulence factor produced by the human pathogen Streptococcus pyogenes and other Streptococcus species. Related “SLS-like” toxins have been characterized in select strains of Clostridium and Listeria, with homologous clusters bioinformatically identified in a variety of other species. SLS is a member of the thiazole/oxazole-modified microcin (TOMM) family of natural products. The structure of SLS has yet to be deciphered and many questions remain regarding its structure-activity relationships. Results: In this work, we assessed the hemolytic activity of a series of C-terminally truncated SLS peptides expressed in SLS-deficient S. pyogenes. Our data indicate that while the N-terminal poly-heterocyclizable (NPH) region of SLS substantially contributes to its bioactivity, the variable C-terminal region of the toxin is largely dispensable. Through genome mining we identified additional SLS-like clusters in diverse Firmicutes, Spirochaetes and Actinobacteria. Among the Spirochaete clusters, naturally truncated SLS-like precursors were found in the genomes of three Lyme disease-causing Borrelia burgdorferi sensu lato (Bbsl) strains. Although unable to restore hemolysis in SLS-deficient S. pyogenes, a Bbsl SLS-like precursor peptide was converted to a cytolysin using purified SLS biosynthetic enzymes. A PCR-based screen demonstrated that SLS-like clusters are substantially more prevalent in Bbsl than inferred from publicly available genome sequences. Conclusions: The mutagenesis data described herein allowed us to define the minimal cytolytic unit of SLS as the NPH region. Interestingly, this region is found in all characterized TOMM cytolysins, as well as the novel putative TOMM cytolysins we discovered. We propose that this conserved region represents the defining feature of the SLS-like TOMM family. We demonstrate the cytolytic potential of a Bbsl SLS-like precursor peptide, which is of similar length to the SLS minimal cytolytic unit, when modified with purified SLS biosynthetic enzymes. As such, we speculate that some Borrelia have the potential to produce a TOMM cytolysin, although the biological significance of this finding remains to be determined. In addition to providing new insight into the structure-activity relationships of SLS, this study greatly expands the cytolysin group of TOMMs.
Contributors: Wang, Steve C., Everson, Philip J., Zhou, Heather Jianan, Park, Dasol, Chudzicki, David J.
... Numerous methods exist for estimating the true stratigraphic range of a fossil taxon based on the stratigraphic positions of its fossil occurrences. Many of these methods require the assumption of uniform fossil recovery potential—that fossils are equally likely to be found at any point within the taxon's true range. This assumption is unrealistic, because factors such as stratigraphic architecture, sampling effort, and the taxon's abundance and geographic range affect recovery potential. Other methods do not make this assumption, but they instead require a priori quantitative knowledge of recovery potential that may be difficult to obtain. We present a new Bayesian method, the Adaptive Beta method, for estimating the true stratigraphic range of a taxon that works for both uniform and non-uniform recovery potential. In contrast to existing methods, we explicitly estimate recovery potential from the positions of the occurrences themselves, so that a priori knowledge of recovery potential is not required. Using simulated datasets, we compare the performance of our method with existing methods. We show that the Adaptive Beta method performs well in that it achieves or nearly achieves nominal coverage probabilities and provides reasonable point estimates of the true extinction in a variety of situations. We demonstrate the method using a dataset of the Cambrian mollusc Anabarella.
Data from: Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe
Contributors: Hoffmann, Alexandra, Plötner, Jörg, Pruvost, Nicolas B. M., Christiansen, Ditte G., Röthlisberger, Sandra, Mikulíček, Peter, Choleva, Lukáš, Cogălniceanu, Dan, Sas-Kovács, István, Shabanov, Dmitry
... Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR) and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed-ploidy populations without any parental species (i.e. all-hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all-hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed.
Data from: Host behavior drives parasite genetics at multiple geographic scales: population genetics of the chewing louse, Thomomydoecus minor
Contributors: Harper, Sheree E., Spradling, Theresa A., Demastes, James W., Calhoun, Courtney S.
... Pocket gophers and their symbiotic chewing lice form a host–parasite assemblage known for a high degree of cophylogeny, thought to be driven by life history parameters of both host and parasite that make host switching difficult. However, little work to date has focused on determining whether these life histories actually impact louse populations at the very fine scale of louse infrapopulations (individuals on a single host) at the same or at nearby host localities. We used microsatellite and mtDNA sequence data to make comparisons of chewing-louse (Thomomydoecus minor) population subdivision over time and over geographic space where there are different potential amounts of host interaction surrounding a zone of contact between two hybridizing pocket-gopher subspecies. We found that chewing lice had high levels of population isolation consistent with a paucity of horizontal transmission even at the very fine geographic scale of a single alfalfa field. We also found marked genetic discontinuity in louse populations corresponding with host subspecies and little, if any, admixture in the louse genetic groups even though the lice are closely related. The correlation of louse infrapopulation differentiation with host interaction at multiple scales, including across a discontinuity in pocket-gopher habitat, suggests that host behaviour is the primary driver of parasite genetics. This observation makes sense in light of the life histories of both chewing lice and pocket gophers and provides a powerful explanation for the well-documented pattern of parallel cladogenesis in pocket gophers and chewing lice.