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opencc-zeroDec 2016View details →

Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach

Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE's accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution.

opencc-zeroDec 2014View details →

Data from: Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid

The effective number of breeders that give rise to a cohort (Nb) is a promising metric for genetic monitoring of species with overlapping generations; however, more work is needed to understand factors that contribute to variation in this measure in natural populations. We tested hypotheses related to interannual variation in Nb in two long-term studies of brook trout populations. We found no supporting evidence for our initial hypothesis that inline image reflects inline image (defined as the number of adults in a population at the time of reproduction). inline image was stable relative to inline image and did not follow trends in abundance (one stream negative, the other positive). We used stream flow estimates to test the alternative hypothesis that environmental factors constrain Nb. We observed an intermediate optimum autumn stream flow for both inline image (R2 = 0.73, P = 0.02) and full-sibling family evenness (R2 = 0.77, P = 0.01) in one population and a negative correlation between autumn stream flow and full-sib family evenness in the other population (r = −0.95, P = 0.02). Evidence for greater reproductive skew at the lowest and highest autumn flow was consistent with suboptimal conditions at flow extremes. A series of additional tests provided no supporting evidence for a related hypothesis that density-dependent reproductive success was responsible for the lack of relationship between Nb and NC (so-called genetic compensation). This work provides evidence that Nb is a useful metric of population-specific individual reproductive contribution for genetic monitoring across populations and the link we provide between stream flow and Nb could be used to help predict population resilience to environmental change.

opencc-zeroApr 2020View details →

Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster

Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short and long-read sequenced to infer the number of PEs in the genomes of dozens of isofemale lines from two Drosophila species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M ´ ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species which suggest there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species-specific.

Data from: Cooperative breeding favours maternal investment in size over number of eggs in spiders

The transition to cooperative breeding may alter maternal investment strategies depending on density of breeders, extent of reproductive skew and allo-maternal care. Change in optimal investment from solitary to cooperative breeding can be investigated by comparing social species with non-social congeners. We tested two hypotheses in a mainly semelparous system: that social, cooperative breeders, compared to subsocial, solitarily breeding congeners, 1) lay fewer and larger eggs because larger offspring compete better for limited resources and become reproducers; 2) induce egg size variation within clutches as a bet-hedging strategy to ensure that some offspring become reproducers. Within two spider genera, Anelosimus and Stegodyphus, we compared species from similar habitats and augmented the results with a mini-meta-analysis of egg numbers depicted in phylogenies. We found that social species indeed laid fewer, larger eggs than subsocials, while egg size variation was low overall, giving no support for bet-hedging. We propose that the transition to cooperative breeding selects for producing few, large offspring because reproductive skew and high density of breeders and young create competition for resources and reproduction. Convergent evolution has shaped maternal strategies similarly in phylogenetically distant species and directed cooperatively breeding spiders to invest in quality rather than quantity of offspring.

Data from: Male body size and condition affects sperm number and production rates in mosquitofish, Gambusia holbrooki

Sperm number is an important predictor of paternity when there is sperm competition. Sperm number is often measured as maximum sperm reserves, but in species where mating is frequent, males will often be replenishing their reserves. Thus, variation in how quickly males can produce sperm is likely to be important in determining male success in sperm competition. Despite this, little is known about how male size, body condition or diet affects sperm production rates. We counted sperm number in large and small Gambusia holbrooki (eastern mosquitofish) after 3 weeks on either a high or low food diet. Sperm number was significantly higher in both larger males and in well-fed males. We then stripped ejaculates again either 1, 2, 3, 4 or 5 days later to investigate subsequent sperm production. The rate of sperm replenishment was influenced by an interaction between size and diet. Large, well-fed males had consistently high levels of sperm available over the 5 days (i.e. rapid replenishment), whereas small poorly fed males showed consistently low levels of sperm availability over the 5 days (i.e. slow replenishment). In contrast, large, poorly fed and small, well-fed males increased their sperm numbers over the first 3 days (i.e. intermediate replenishment). Our study highlights that when mating is frequent and sperm competition is high, size and condition dependence of maximal sperm number and of sperm production rate might both contribute to variation in male reproductive success.

Data from: Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis

Background: Mycoplasma bovis is an important pathogen causing pneumonia, mastitis and arthritis in cattle worldwide. As this agent is primarily transmitted by direct contact and spread through animal movements, efficient genotyping systems are essential for the monitoring of the disease and for epidemiological investigations. The aim of this study was to compare and evaluate the multi locus sequence typing (MLST) and the multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) through the genetic characterization of M. bovis isolates from Hungary. Results: Thirty one Hungarian M. bovis isolates grouped into two clades by MLST. Two strains had the same sequence type (ST) as reference strain PG45, while the other twenty nine Hungarian isolates formed a novel clade comprising five subclades. Isolates originating from the same herds had the same STs except for one case. The same isolates formed two main clades and several subclades and branches by MLVA. One clade contained the reference strain PG45 and three isolates, while the other main clade comprised the rest of the strains. Within-herd strain divergence was also detected by MLVA. Little congruence was found between the results of the two typing systems. Conclusions: MLST is generally considered an intermediate scale typing method and it was found to be discriminatory among the Hungarian M. bovis isolates. MLVA proved to be an appropriate fine scale typing tool for M. bovis as this method was able to distinguish closely related strains isolated from the same farm. We recommend the combined use of the two methods for the genotyping of M. bovis isolates. Strains have to be characterized first by MLST followed by the fine scale typing of identical STs with MLVA.

opencc-zeroDec 2015View details →

Data from: Effects of pollination intensity on offspring number and quality in a wind-pollinated herb

Low pollination intensity may cause low seed set in plant populations and is thought to be responsible for evolutionary transitions from outcrossing to selfing, or from animal to wind pollination. Variation in pollination intensity may also affect seed quality both through its influence on the degree of pollen competition (with lower quality offspring produced under low pollen intensities) and through seed size–number trade-offs (with plants under low pollination intensity producing fewer but larger seeds). Here, we use a field experiment to examine the effects of pollination intensity on both quantity and quality of progeny. We manipulated pollen receipt to stigmas of the wind-pollinated dioecious plant Mercurialis annua by varying the distance of females from males. We then compared seed size and number, seedling growth and allocation to male and female function, for the progeny produced by females subjected to different pollination intensities. Our experiment revealed a reduction in pollen load with increasing distance to males, translating into large reductions in the number of seeds produced but only small effects on the performance of offspring. The main effect on offspring quality was through a seed size–number trade-off, with pollen-limited females producing fewer but larger seeds, which subsequently performed better. Sons and daughters were affected differently by this trade-off, pointing to gender-dependent effects of pollination intensity on progeny performance. Synthesis. Our results highlight the importance of pollination intensity on both the quantity and quality of progeny. Nevertheless, fitness calculations suggest that the enhanced quality of seed produced by pollen-limited mothers was not sufficient to offset their losses in terms of quantity.

opencc-zeroDec 2016View details →

Data from: Distribution and functionality of copy number variation across European cattle populations

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.

Data from: Dynamics of copy number variation in host races of the pea aphid

Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Grs and Ors, respectively), in the process of host race formation. We used targeted re-sequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors, and a decrease in the probability of complete gene duplication or deletion (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Grs were over-represented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.

opencc-zeroDec 2016View details →

Data from: Cooperative breeding influences the number and type of vocalizations in avian lineages

Although communicative complexity is often predicted to correlate with social complexity in animal societies, few studies have employed large-scale comparative analyses to test whether socially complex species have more complex systems of communication. I tested this social complexity hypothesis in birds (Class: Aves) using the large amount of natural history information that describes both vocal repertoire and social system in these species. To do so, I marshalled data from primary and secondary records of avian vocal repertoires (n = 253), and for each of the species in the dataset I recorded the reported repertoire size and associated species information. Using phylogenetic comparative methods, I found that cooperative breeding was a strong and repeatable predictor of vocal repertoire size, while other social variables, e.g. group size and group stability, had little or no influence on repertoire size. Importantly, repertoire sizes expanded concurrently with the evolution of cooperative breeding, suggesting a direct link between these two traits. Cooperatively breeding species devoted significantly more of their repertoire to contact calls and alarm calls. Overall, these results therefore lend support to the hypothesis that social complexity via behavioural coordination leads to increases in vocal complexity.

FIGURE 32 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURE 32. Phylogenetic position of Crozetia based on morphology. Characterstates 1 21 are as discussed by Currie and Grimaldi (2000); characterstates 22 24 are also from Currie & Grimaldi (loc. cit.), but are reoptimized in view of discussion in text.

FIGURE 31 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURE 31. Histogram of frequency of larval head widths showing probable instars of Crozetia seguyi. Outliers to the extreme right Cr. crozetensis last instar.

FIGURES 1112. Crozetia female adult pretarsal claws and basal tooth. 11 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 1112. Crozetia female adult pretarsal claws and basal tooth. 11. Cr. crozetensis. 12. Cr. seguyi. Scale bar = 0.02 mm.

FIGURES 2027. Crozetia larval structures. 20 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 2027. Crozetia larval structures. 20. Cr. crozetensis, LM of last instar larval hypostoma. Scale bar = 0.1 mm. 21. Cr. seguyi, SEM of last instar larval hypostoma. Image foreshortened see Fig 23. Scale bar = 0.05 mm. 22. Cr. crozetensis, LM of last instar larval hypostoma and postgenal cleft. Scale bar = 0.1 mm. 23. Cr. seguyi, LM of last instar larval hypostoma and postgenal cleft. Scale bar = 0.1 mm. 24. Cr. crozetensis, LM of abdomen, last instar larvae. Scale bar = 1.0 mm. 25. Cr. seguyi, LM of abdomen, last instar larvae. Scale bar = 1.0 mm. 26. Cr. crozetensis, last instar, anal sclerites. Scale bar = 0.1 mm. 27. Cr. seguyi, last instar, anal sclerites. Scale bar = 0.1 mm.

FIGURES 710. Crozetia adult genitalia. 7 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 710. Crozetia adult genitalia. 7. Cr. crozetensis, male, ventral (left), and lateral views (right) of ventral plate and gonostylus. Scale bar = 0.2 mm. 8. Cr. seguyi, male. Scale bar = 0.2 mm. 9. Cr. crozetensis, female, ventral view, insert lateral view of anal lobe and cercus. Scale bar = 0.2 mm. 10. Cr. seguyi, female. Scale bar = 0.2 mm. Abbreviations: adm aedeagal membrane; anlb anal lobe; anm anal membrane; c cercus; gc gonocoxa; gs gonostylus; hypv hypogynial valve; p paramere; spm spermatheca; vp ventral plate.

FIGURES 2830 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 2830. Mouthparts of first instar Crozetia seguyi larvae. 28. Labral fan. Scale bar = 0.02 mm. 29. Larval hypostoma. Scale bar = 0.02 mm. 30. Larval mandibles. Scale bar = 0.02 mm. Abbreviations: lb labral fan; hyps hypostoma; mnd mandible.

FIGURES 15-19. Crozetia. 15 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 15-19. Crozetia. 15. Cr. crozetensis, male paratype wing. Scale bar = 0.5 mm. 16. Cr. seguyi, higher magnification of male wing base. Scale bar = 0.5 mm. 17. Cr. seguyi, SEM of last instar larval head, frontal view. Scale bar = 0.1 mm. 18. Cr. crozetensis, LM of last instar larval head, dorsal view. Scale bar = 0.1 mm. 19. Cr. seguyi, LM of last instar larval head, dorsal view. Scale bar = 0.1 mm. Abbreviations: ant - antenna; ca - cephalic apotome; lf - labral fan; hyps - hypostoma; mnd - mandible; mx - maxilla; mxp - maxillary palpus.

FIGURES 13-14. Crozetia pupae. Left lateral views. 13 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 13-14. Crozetia pupae. Left lateral views. 13. Cr. crozetensis. 14. Cr. seguyi. Note rudimentary cocoon on posterior. Scale bar = 1.0 mm.

FIGURE 3 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURE 3. Rivière du Camp, Possession Island, Crozet Islands, 1979. A typical habitat of Crozetia larvae. Pic du Mascarin (alt. 934 m) is in the background. (Courtesy, L. Davies).

FIGURE 2 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURE 2. Islands of the Crozet Archipelago. Bathymetric contours in meters. (Adapted from Boudon and Nougier 1982).