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Data from: A structured population model suggests that long life and post-reproductive lifespan promote the evolution of cooperation

Social organization correlates with longevity across animal taxa. This correlation has been explained by selection for longevity by social evolution. The reverse causality is also conceivable but has not been sufficiently considered. We constructed a simple, spatially structured population model of asexually reproducing individuals to study the effect of temporal life history structuring on the evolution of cooperation. Individuals employed fixed strategies of cooperation or defection towards all neighbours in a basic Prisoner׳s Dilemma paradigm. Individuals aged and transitioned through different life history stages asynchronously without migration. An individual׳s death triggered a reproductive event by one immediate neighbour. The specific neighbour was chosen probabilistically according to the cumulative payoff from all local interactions. Varying the duration of pre-reproductive, reproductive, and post-reproductive life history stages, long-term simulations allowed a systematic evaluation of the influence of the duration of these specific life history stages. Our results revealed complex interactions among the effects of the three basic life history stages and the benefit to defect. Overall, a long post-reproductive stage promoted the evolution of cooperation, while a prolonged pre-reproductive stage has a negative effect. In general, the total length of life also increased the probability of the evolution of cooperation. Thus, our specific model suggests that the timing of life history transitions and total duration of life history stages may affect the evolution of cooperative behaviour. We conclude that the causation of the empirically observed association of life expectancy and sociality may be more complex than previously realized.

Data from: Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program

While the goal of supplementation programs is to provide positive, population-level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive-born individuals are fully integrated into the natural population. In order to evaluate the long-term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook salmon (Oncorhynchus tshawytscha), we genotyped tissue samples spanning a 19-year period (1998-2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho USA. We expanded upon previous estimates of relative reproductive success (RRS) to include two full generations and used generalized linear models to determine if origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural-origin broodstock provided a long-term demographic boost to the population (mean of 4.56 times in the 1st generation and mean of 2.52 times in the 2nd generation). Overall when spawning in nature, hatchery-origin fish demonstrated a trend towards lower RS compared to natural-origin fish (p<0.05). However, when hatchery-origin fish successfully spawned with natural-origin fish, they had similar RS compared to natural by natural crosses (1st generation mean hatchery by natural cross RRS = 1.11 females, 1.13 males; 2nd generation mean hatchery by natural cross RRS = 1.03 females, 1.08 males). While origin, return year, and body length were significant predictors of fitness for both males and females (p<0.05), return day was significant for males but not females (p>0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long-term fitness effects on wild populations.

opencc-zeroDec 2015View details →

Data from: How do growth and sibling competition affect telomere dynamics in the first month of life of long-lived seabird?

Telomeres are nucleotide sequences located at the ends of chromosomes that promote genome stability. Changes in telomere length (dynamics) are related to fitness or life expectancy, and telomere dynamics during the development phase are likely to be affected by growth and stress factors. Here, we examined telomere dynamics of black-tailed gull chicks (Larus crassirostris) in nests with and without siblings. We found that the initial telomere lengths of singletons at hatching were longer than those of siblings, indicating that singletons are higher-quality chicks than siblings in terms of telomere length. Other factors likely affecting individual quality (i.e., sex, laying date, laying order of eggs, and clutch size) were not related to telomere lengths. Within broods, initial telomere lengths were longer in older chicks than in younger chicks, suggesting that maternal effects, which vary with laying sequence, influence the initial lengths. Additionally, telomeres of chicks with a sibling showed more attrition between hatching and fledging than those of singleton chicks, suggesting that being raised with siblings can cause a sustained competitive environment that leads to telomere loss. High growth rates were associated with a low degree of telomere shortening observed in older siblings, perhaps because slower growth reflects higher food stress and/or higher aerobic metabolism from increased begging effort. Our results show that developmental telomere attrition was an inevitable consequence in two-chick nests in the pre- and post-hatching microenvironments due to the combination of social stress within the nest and maternal effects. The results of our study shed light on telomere dynamics in early life, which may represent an important physiological undercurrent of life-history traits.

opencc-zeroDec 2015View details →

Data from: Actuarial senescence in a long-lived orchid challenges our current understanding of ageing

The dominant evolutionary theory of actuarial senescence—an increase in death rate with advancing age—is based on the concept of a germ cell line that is separated from the somatic cells early in life. However, such a separation is not clear in all organisms. This has been suggested to explain the paucity of evidence for actuarial senescence in plants. We used a 32 year study of Dactylorhiza lapponica that replaces its organs each growing season, to test whether individuals of this tuberous orchid senesce. We performed a Bayesian survival trajectory analysis accounting for reproductive investment, for individuals under two types of land use, in two climatic regions. The mortality trajectory was best approximated by a Weibull model, showing clear actuarial senescence. Rates of senescence in this model declined with advancing age, but were slightly higher in mown plots and in the more benign climatic region. At older ages, senescence was evident only when accounting for a positive effect of reproductive investment on mortality. Our results demonstrate actuarial senescence as well as a survival–reproduction trade-off in plants, and indicate that environmental context may influence senescence rates. This knowledge is crucial for understanding the evolution of demographic senescence and for models of plant population dynamics.

Data from: A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food

Background: Mate finding and recognition in animals evolves during niche adaptation and involves social signals and habitat cues. Drosophila melanogaster and related species are known to be attracted to fermenting fruit for feeding and egg-laying, which poses the question of whether species-specific fly odours contribute to long-range premating communication. Results: We have discovered an olfactory channel in D. melanogaster with a dual affinity to sex and food odorants. Female flies release a pheromone, (Z)-4-undecenal (Z4-11Al), that elicits flight attraction in both sexes. Its biosynthetic precursor is the cuticular hydrocarbon (Z,Z)-7,11-heptacosadiene (7,11-HD), which is known to afford reproductive isolation between the sibling species D. melanogaster and D. simulans during courtship. Twin olfactory receptors, Or69aB and Or69aA, are tuned to Z4-11Al and food odorants, respectively. They are co-expressed in the same olfactory sensory neurons, and feed into a neural circuit mediating species-specific, long-range communication; however, the close relative D. simulans, which shares food resources with D. melanogaster, does not respond to Z4-11Al. Conclusion: The Or69aA and Or69aB isoforms have adopted dual olfactory traits. The underlying gene yields a collaboration between natural and sexual selection, which has the potential to drive speciation.

Data from: Immunocompetence in a long-lived ectothermic vertebrate is temperature dependent but shows no decline in older adults

1. Temperature affects nearly all aspects of the physiology of ectotherms, including their ability to mount an immune response. Typically, the ectothermic vertebrate immune system can respond over a wide range of temperatures, but there is a species-specific temperature at which responses are strongest, with impaired responses above and below this threshold. In long-lived ectotherms, aging could also influence the ability to respond to temperature changes as immunosenecence, the functional decrease in immune function with age, is widely reported. 2. This study examined the effects of the interaction between temperature and age on B cell function in a long-lived reptile, the red-eared slider turtle, Trachemys scripta. B cells in this species have previously been shown to have two main functions, phagocytosis and antibody production. 3. Adult turtles were trapped and blood samples taken. Because sliders grow throughout their lifetime, plastron length was used as a proxy for age. Leukocytes were isolated and used in either an ELISpot assay to examine their ability to produce antibodies spontaneously or when stimulated, or used in a phagocytic assay. The ELISpot and phagocytic assays were conducted over a range of biologically relevant temperatures. 4. We found no interaction between age and temperature on any measure of B cell function. In all cases there was a significant effect of temperature, with impaired function at temperatures below 29°C, but no impairment of function at higher temperatures. We also found little evidence of immunosenesce in any response. 5. This study provides insight into the thermal biology of B cell function in sliders and provides an interesting connection between immunology, behavior, and ecology in this long-lived turtle.

Data from: Slow development as an evolutionary cost of long life

Life-history theory predicts a trade-off between early-life fitness and life span. While the focus traditionally has been on the fecundity-life span trade-off, there are strong reasons to expect trade-offs with growth rate and/or development time. We investigated the roles of growth rate and development time in the evolution of life span in two independent selection experiments in the outcrossing nematode Caenorhabditis remanei. First, we found that selection under heat-shock leads to the evolution of increased life span without fecundity costs, but at the cost of slower development. Thereafter, the putative evolutionary links between development time, growth rate, fecundity, heat-shock resistance and life span were independently assessed in the second experiment by directly selecting for fast or slow development. This experiment confirmed our initial findings, since selection for slow development resulted in the evolution of long life span and increased heat-shock resistance. Because there were no consistent trade-offs with growth rate or fecundity, our results highlight the key role of development rate – differentiation of the somatic cells per unit of time – in the evolution of life span. Since development time is under strong selection in nature, reduced somatic maintenance resulting in shorter life span may be a widespread cost of rapid development.

Data from: An exceptionally preserved association of complete dinosaur skeletons reveals the oldest long-necked sauropodomorphs

The rise of sauropodomorphs is still poorly understood due to the scarcity of well-preserved fossils in early Norian rocks. Here, we present an association of complete and exceptionally well-preserved dinosaur skeletons that helps filling that gap. They represent a new species, which is recovered as member of a clade solely composed of Gondwanan Triassic taxa. The new species allows defining a set of anatomical changes that shaped sauropodomorph evolution along a period from 233–225 Ma, as recorded in the well dated Late Triassic beds of Brazil. In that time span, apart from achieving a more herbivorous diet, sauropodomorph dinosaurs increased their size in a ratio of 230% and their typical long neck was also established, becoming proportionally twice longer than those of basal taxa. Indeed, the new dinosaur is the oldest-known sauropodomorph with such an elongated neck, suggesting that the ability to feed on high vegetation was a key trait achieved along the early Norian. Finally, the clustered preservation mode of the skeletons represents the oldest evidence of gregarious behaviour among sauropodomorphs.

Data from: Population density and climate shape early-life survival and recruitment in a long-lived pelagic seabird

1. Our understanding of demographic processes is mainly based on analyses of traits from the adult component of populations. Early-life demographic traits are poorly known mainly for methodological reasons. Yet, survival of juvenile and immature individuals is critical for the recruitment into the population and thus for the whole population dynamic, especially for long-lived species. This bias currently restrains our ability to fully understand population dynamics of long-lived species and life-history theory. 2. The goal of this study was to estimate the early-life demographic parameters of a long-lived species with a long immature period (9–10 years), to test for sex and age effects on these parameters and to identify the environmental factors encountered during the period of immaturity that may influence survival and recruitment. 3. Using capture–mark–recapture multievent models allowing us to deal with uncertain and unobservable individual states, we analysed a long-term data set of wandering albatrosses to estimate both age- and sex-specific early-life survival and recruitment. We investigated environmental factors potentially driving these demographic traits using climatic and fisheries covariates and tested for density dependence. 4. Our study provides for the first time an estimate of annual survival during the first 2 years at sea for an albatross species (0·801 ± 0·014). Both age and sex affected early-life survival and recruitment processes of this long-lived seabird species. Early-life survival and recruitment were highly variable across years although the sensitivity of young birds to environmental variability decreased with age. Early-life survival was negatively associated with sea surface temperature, and recruitment rate was positively related to both Southern Annular Mode and sea surface temperature. We found strong evidence for density-dependent mortality of juveniles. Population size explained 41% of the variation of this parameter over the study period. 5. These results indicate that early-life survival and recruitment were strongly age and sex dependent in a dimorphic long-lived species. In addition, early-life demographic parameters were affected by natal environmental conditions and by environmental conditions faced during the period of immaturity. Finally, our results constitute one of the first demonstrations of density dependence on juvenile survival in seabirds, with major consequences for our understanding of population dynamics in seabirds.

Data from: High virulence sub-populations in Pseudomonas aeruginosa long-term cystic fibrosis airway infections

Background: Pseudomonas aeruginosa typically displays loss of virulence-associated secretions over the course of chronic cystic fibrosis infections. This has led to the suggestion that virulence is a costly attribute in chronic infections. However, previous reports suggest that overproducing (OP) virulent pathotypes can coexist with non-producing mutants in the CF lung for many years. The consequences of such within-patient phenotypic diversity for the success of this pathogen are not fully understood. Here, we provide in-depth quantification of within-host variation in the production of three virulence associated secretions in the Liverpool cystic fibrosis epidemic strain of P. aeruginosa, and investgate the effect of this phenotypic variation on virulence in acute infections of an insect host model. Results: Within-patient variation was present for all three secretions (pyoverdine, pyocyanin and LasA protease). In two out of three patients sampled, OP isolates coexisted with under-producing mutants. In the third patient, all 39 isolates were under-producers of all three secretions relative to the transmissible ancestor LESB58. Finally, this phenotypic variation translated into variation in virulence in an insect host model. Conclusions: Within population variation in the production of P. aeruginosa virulence-associated secretions can lead to high virulence sub-populations persisting in patients with chronic CF infections.

Data from: Beyond novelty effect: a mixed-methods exploration into the motivation for long-term activity tracker use

Objectives: Activity trackers hold the promise to support people in managing their health through quantified measurements about their daily physical activities. Monitoring personal health with quantified activity tracker-generated data provides patients with an opportunity to self-manage their health. Many activity tracker user studies have been conducted within short time frames, however, which makes it difficult to discover the impact of the activity tracker's novelty effect or the reasons for the device's long-term use. This study explores the impact of novelty effect on activity tracker adoption and the motivation for sustained use beyond the novelty period. Materials and Methods: This study uses a mixed-methods approach that combines both quantitative activity tracker log analysis and qualitative one-on-one interviews to develop a deeper behavioral understanding of 23 Fitbit device users who have used their trackers for at least two months (range of use = 69 - 1073 days). Results: Log data from users' Fitbit devices revealed two stages in their activity tracker use: the novelty period and the long-term use period. The novelty period for Fitbit users in this study was approximately three months, during which they might have discontinued using their devices. Discussion: The qualitative interview data identified various factors that motivate users to continuously use Fitbit devices in different stages. The discussion of these results provides design implications to guide future development of activity tracking technology. Conclusion: This study reveals important dynamics emerging over long-term activity tracker use, contributes new knowledge to consumer health informatics and human-computer interaction, and offers design implications to guide future development of similar health-monitoring technologies that better account for long-term use in support of patient care and health self-management.

Data from: Evidence for long-term shift in plant community composition under decadal experimental warming

Summary: 1. Long-term, slow ecological processes such as changes in plant community structure and composition strongly regulate ecosystem responses to climate change. Shifts in plant community are expected in chronically altered environments under warming. However, experimental evidence for long-term shifts and the associated mechanisms is still scarce in temperate grasslands. 2. Here, we explore the long-term responses of a prairie plant community to 14-year (2000-2013) manipulations of climate warming and clipping in Oklahoma, USA. Infrared heaters were used to elevate soil temperature by about 2 ºC all year round and annual clipping was applied to mimic hay harvest. 3. Community composition was resistant to experimental warming in the first seven years, but started to show responses starting from the eighth year; clipping consistently affected community composition over the years. Compositional change under long-term warming was mainly due to one invasive species and three dominant species. The negative correlations in relative abundance between the invasive species and the dominant species suggest inter-specific competition. Community structure (i.e., richness, evenness and diversity) had no overall response to experimental warming. However, in 2007, the extreme wet year, warming reduced species richness by 30%. Clipping promoted species richness by 10% on average over the 14 years but decreased community evenness. Warming did not interact with clipping in influencing the plant community variables. 4. Synthesis: Our study provides experimental evidence for long-term shifts in plant community composition due to warming and revealed novel mechanisms (i.e., species invasion and associated biotic interactions) underlying the long-term shift. The results also suggest that climate extremes may elicit or advance community responses to climate warming. The findings highlight that long-term climate change experiments are essential to reveal potential shifts in community composition.

Data from: Unified pre- and postsynaptic long-term plasticity enables reliable and flexible learning

Although it is well known that long-term synaptic plasticity can be expressed both pre- and postsynaptically, the functional consequences of this arrangement have remained elusive. We show that spike-timing-dependent plasticity with both pre- and postsynaptic expression develops receptive fields with reduced variability and improved discriminability compared to postsynaptic plasticity alone. These long-term modifications in receptive field statistics match recent sensory perception experiments. Moreover, learning with this form of plasticity leaves a hidden postsynaptic memory trace that enables fast relearning of previously stored information, providing a cellular substrate for memory savings. Our results reveal essential roles for presynaptic plasticity that are missed when only postsynaptic expression of long-term plasticity is considered, and suggest an experience-dependent distribution of pre- and postsynaptic strength changes.

Data from: Flexibility, variability and constraint in energy management strategies across vertebrate taxa revealed by long-term heart rate measurements

1) Animals are expected to be judicious in the use of the energy they gain due to the costs and limits associated with its intake. The management of energy expenditure (EE) exhibited by animals has previously been considered in terms of three patterns: the constrained, independent and performance patterns of energy management. These patterns can be interpreted by regressing daily EE against maintenance EE measured over extended periods. From the multiple studies on this topic, there is equivocal evidence about the existence of universal patterns in certain aspects of energy management. 2) The implicit assumption that animals exhibit specifically one of three discrete energy management patterns, and without variation, seems simplistic. We suggest that animals can exhibit gradations of different energy management patterns and that the exact pattern will fluctuate as their environmental context changes. 3) To investigate these ideas, and for possible large-scale patterns in energy management pattern, we analysed long-term heart rate data – a strong proxy for EE – across and within individuals in 16 species of birds, mammals, and fish. 4) Our analyses of 292 individuals representing 46 539 observation-days suggest that vertebrates typically exhibit predominantly the independent or performance energy patterns at the across-individual level, and that the pattern does not associate with taxonomic group. Within individuals, however, animals generally exhibit some degree of energy constraint. Together, these findings indicate that across diverse species, some individuals supply more energy to all aspects of their life than do others, however all individuals must trade-off deployment of their available energy between competing functions. This demonstrates that within-individual analyses are essential for interpretation of energy management patterns. 5) We also found that species do not necessarily exhibit a fixed energy management pattern but rather temporal variation in their energy management over the year. Animals' energy management exhibited stronger energy constraint during periods of higher EE, which typically coincided with clear and key life cycle events such as reproduction, suggesting an adaptive plasticity to respond to fluctuating energy demands.

Data from: Reduced telomere length in offspring of old fathers in a long-lived seabird

Evidence for transgenerational effects of senescence, whereby offspring from older parents have a reduced lifetime reproductive success, is increasing. Such effects could arise from compromised germline maintenance in old parents, potentially reflected in reduced telomere length in their offspring. We test the relationship between parental age and offspring early-life telomere length in a natural population of common terns and find a significant negative correlation between paternal age and offspring telomere length. Offspring telomere length is reduced by 35 base pairs for each additional year of paternal age. We find no correlation with maternal age. These results fit with the idea of compromised germline maintenance in males, whose germline stem cells require continued division.

Data from: Growth potential can affect timing of maturity in a long-lived semelparous fish

Many diadromous fishes such as salmon and eels that move between freshwater and the ocean have evolved semelparous reproductive strategies, but both groups display considerable plasticity in characteristics. Factors such as population density and growth, predation risk or reproduction cost have been found to influence timing of maturation. We investigated the relationship between female size at maturity and individual growth trajectories of the long-lived semelparous European eel, Anguilla anguilla. A Bayesian model was applied to 338 individual growth trajectories of maturing migration-stage female silver eels from France, Ireland, the Netherlands, and Hungary. The results clearly showed that when growth rates declined, the onset of maturation was triggered, and the eels left their growth habitats and migrated to the spawning area. Therefore, female eels tended to attain larger body size when the growth conditions were good enough to risk spending extra time in their growth habitats. This flexible maturation strategy is likely related to the ability to utilize diverse habitats with widely ranging growth and survival potentials in the catadromous life-history across its wide species range.

opencc-zeroJun 2019View details →

Data from: Accounting for long-term directional trends on year-to-year synchrony in species fluctuations

What determines the stability of communities under environmental fluctuations remains one of the most debated questions in ecology. Scholars generally agree that the similarity in year-to-year fluctuations between species is an important determinant of this stability. Concordant fluctuations in species abundances through time (synchrony) decrease stability while discordance in fluctuations (anti-synchrony) should stabilize communities. Researchers have interpreted the community-wide degree of synchrony in temporal fluctuations as the outcome of different processes. However, existing synchrony measures depend not only on year-to-year species fluctuations, but also on long-term directional trends in species composition, for example due to land-use or climate change. The neglected effect of directional trends in species composition could cause an increase in synchrony that is not due to year-to-year fluctuations, as species that simultaneously increase (or decrease) in abundance over time will appear correlated, even if they fluctuate discordantly from year to year. The opposite pattern is also conceivable, where different species show contrasting trends in their abundances, thus overestimating year-to-year anti-synchrony. Therefore, trends in species composition may limit our understanding of potential ecological mechanisms behind synchrony between species. We propose two easily implementable solutions, with corresponding R functions, for testing and accounting for the effect of trends in species composition on overall synchrony. The first approach is based on computing synchrony over the residuals of fitted species trends over time. The second approach, applicable to already existing indices, is based on three-terms local variance, i.e. computing variance over three-years-long, movable windows. We demonstrate these methods using simulations and data from real plant communities under long-term directional changes, discussing when one approach can be preferred. We show that accounting for long-term temporal trends is both necessary and that separation of effect of trends and year-to-year fluctuation provides a better understanding of ecological mechanisms and their connections with ecological theory.

opencc-zeroDec 2008View details →

Data from: Testing hypotheses of chaetognath origins: long branches revealed by 18S ribosomal DNA

Many hypotheses regarding the phylogenetic position of the Chaetognatha (arrow worms) have been proposed; these organisms are problematic primarily because their morphology offers few unambiguous systematic characters that ally them with other taxa. Early researchers proposed a plethora of phylogenetic placements for the Chaetognatha, grouping them with such divergent taxa as acanthocephalans and mollusks, but more traditional hypotheses posit that chaetognaths are, in fact, deuterostomes. Recently, Telford and Holland (1993, Mol. Biol. Evol. 10:660--676) and Wada and Satoh (1994, Proc. Natl. Acad. Sci. USA 91:1801--1804) disputed the deuterostome affinities of chaetognaths based on 18S nuclear ribosomal RNA (rDNA) gene sequence data. By employing published 18S rDNA gene sequence data, I extended these previous analyses by testing specific hypotheses of chaetognath affinities to nematodes, mollusks, acanthocephalans, and deuterostomes. Both parsimony and neighbor-joining analyses supported the monophyly of a chaetognath--nematode clade. Faith's T-PTP test and winning-sites analyses were employed to discriminate among competing hypotheses. The possibility of long-branch attraction accounting for the chaetognath--nematode relationship was explored by analyzing alternative four-taxon trees. An evolutionary scenario for the origin of the chaetognath lineage from a vermiform benthic organism is presented.

opencc-zeroDec 2018View details →

Data from: Competition is crucial for social comparison processes in long-tailed macaques

Humans modulate their self-evaluations and behaviour as a function of conspecific presence and performance. In this study we tested for the presence of human-like social comparison effects in long-tailed macaques (Macaca fascicularis). The monkeys' task was to extract food from an apparatus by pulling drawers within reach and we measured latency between drawer-pulls. Subjects either worked on the task with a partner who could access the apparatus from an adjacent cage, worked in the absence of a conspecific but with food moving towards the partner's side or worked next to a partner who was denied apparatus access. We further manipulated partner performance and competitiveness of the setup. We found no indication that long-tailed macaques compare their performance to the performance of conspecifics. They were not affected by the mere presence of the partner but they paid close attention to the partner's actions when they were consequential for food availability. If social comparison processes are present in long-tailed macaques, the present study suggests they may only manifest in situations involving direct competition and would thus be different from social comparisons in humans, which manifest also in the absence of direct competition, for example in evaluative contexts.

Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.