The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.

https://www.jstor.org/stable/10.1086/343873

Phylogenetic analysis and comparative data: a test and review of evidence

Knowledge of the ecological and evolutionary causes of dispersal can be crucial in understanding the behaviour of spatially structured populations, and predicting how species respond to environmental change. Despite the focus of much theoretical research, simplistic assumptions regarding the dispersal process are still made. Dispersal is usually regarded as an unconditional process although in many cases fitness gains of dispersal are dependent on environmental factors and individual state. Condition-dependent dispersal strategies will often be superior to unconditional, fixed strategies. In addition, dispersal is often collapsed into a single parameter, despite it being a process composed of three interdependent stages: emigration, inter-patch movement and immigration, each of which may display different condition dependencies. Empirical studies have investigated correlates of these stages, emigration in particular, providing evidence for the prevalence of conditional dispersal strategies. Ill-defined use of the term ‘dispersal’, for movement across many different spatial scales, further hinders making general conclusions and relating movement correlates to consequences at the population level. Logistical difficulties preclude a detailed study of dispersal for many species, however incorporating unrealistic dispersal assumptions in spatial population models may yield inaccurate and costly predictions. Further studies are necessary to explore the importance of incorporating specific condition-dependent dispersal strategies for evolutionary and population dynamic predictions.

https://onlinelibrary.wiley.com/doi/pdf/10.1017/S1464793104006645

Causes and consequences of animal dispersal strategies: relating individual behaviour to spatial dynamics.

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.

https://serval.unil.ch/resource/serval:BIB_2A4C7F8DA305.P001/REF.pdf

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

In his introduction to this detailed survey of knowledge of insect societies, the author points out that research on insect sociology has proceeded in three phases, the natural history phase, the physiological phase and the population-biology phase. Advances in the first two phases have permitted embarkation in the third phase on a more rigorous theory of social evolution based on population genetics and writing this book, the author wished to relate the three phases of research on insects and to express insect sociology as population biology. A glossary of terms, a considerable bibliography and a general index are included. Other CABI sites 

The Insect Societies

There is accumulating evidence that individuals leave their natal area and select a breeding habitat non-randomly by relying upon information about their natal and future breeding environments. This variation in dispersal is not only based on external information (condition dependence) but also depends upon the internal state of individuals (phenotype dependence). As a consequence, not all dispersers are of the same quality or search for the same habitats. In addition, the individual's state is characterized by morphological, physiological or behavioural attributes that might themselves serve as a cue altering the habitat choice of conspecifics. These combined effects of internal and external information have the potential to generate complex movement patterns and could influence population dynamics and colonization processes. Here, we highlight three particular processes that link condition-dependent dispersal, phenotype-dependent dispersal and habitat choice strategies: (1) the relationship between the cause of departure and the dispersers' phenotype; (2) the relationship between the cause of departure and the settlement behaviour and (3) the concept of informed dispersal, where individuals gather and transfer information before and during their movements through the landscape. We review the empirical evidence for these processes with a special emphasis on vertebrate and arthropod model systems, and present case studies that have quantified the impacts of these processes on spatially structured population dynamics. We also discuss recent literature providing strong evidence that individual variation in dispersal has an important impact on both reinforcement and colonization success and therefore must be taken into account when predicting ecological responses to global warming and habitat fragmentation.

Informed dispersal, heterogeneity in animal dispersal syndromes and the dynamics of spatially structured populations

Preface Acknowledgements 1. Introduction to the Bathyergidae 2. The subterranean niche 3. The food resource of African Mole-Rats 4. Social organisation in African Mole-Rats 5. Life history patterns and reproductive biology 6. Social suppression of reproduction in African Mole-Rats 7. The genetic structure of Mole-Rat populations 8. The evolution of sociality on African Mole-Rats References Index.

African Mole-Rats: Ecology and Eusociality

CLOSE inbreeding is known for a variety of small mammal species1–4 for which a high probability of mortality during dispersal makes helping and delayed maturation a relatively secure fitness option5. Prolonged inbreeding, however, is usually associated with lowered fitness6,7, and it has been shown that most highly inbred small mammals8 and social insects9 have inbreeding-avoidance mechanisms that promote some degree of outbreeding. However, previous field and laboratory research on the naked mole-rat (Heterocephalm glaber) suggested that this cooperatively breeding rodent is highly inbred10–12, with new colonies forming by fission13. Here we report the discovery of a dispersal phenotype that may occasionally promote outbreeding in naked mole-rats. These dispersers are morphologically, physiologically and behaviourally distinct from other colony members. They are laden with fat, exhibit elevated levels of luteinizing hormone, have a strong urge to disperse, and only solicit matings with non-colony members. These findings suggest that, although rare, a dispersive morph exists within naked mole-rat colonies.

A dispersive morph in the naked mole-rat.

The African mole-rats (family Bathyergidae) are subterranean hystricomorph rodents occurring in a variety of habitats and displaying levels of sociality which range from solitary to eusocial, making them a unique mammalian taxonomic group to test ecological influences on sociality. Here, we use an extensive DNA-based phylogeny and comparative analysis to investigate the relationship between ecology, sociality and evolution within the family. Mitochondrial cytochrome-b and 12s rRNA trees reveal that the solitary species are monophyletic when compared to the social species. The naked mole-rat (Heterocephalus glaber) is ancestral and divergent from the Damaraland mole-rat (Cryptomys damarensis), supporting previous findings that have suggested the multiple evolution of eusociality within the family. The Cryptomys genus is species-rich and contains taxa exhibiting different levels of sociality, which can be divided into two distinct clades. A total of seven independent comparisons were generated within the phylogeny, and three ecological variables were significantly correlated with social group size: geophyte density (p < 0.05), mean months per year of rainfall greater than 25 mm (p < 0.001), and the coefficient of rainfall variation (p = 0.001). These results support the food-aridity hypothesis for the evolution of highly social cooperative behaviour in the Bathyergidae, and are consistent with the current theoretical framework for skew theory.

https://www.jstor.org/stable/pdfplus/50771.pdf

Ecological constraints drive social evolution in the African mole-rats.

Naked mole–rat colonies exhibit a high reproductive skew, breeding being typically restricted to one female (the ‘queen’) and one to three males. Other colony members are reproductively suppressed, although this suppression can be reversed following the removal or death of the queen. We examined dominance and queen succession within captive colonies to investigate the relationship between urinary testosterone and cortisol, dominance rank and reproductive status; and to determine if behavioural and/or physiological parameters can be used as predictors of queen succession. Social structure was characterized by a linear dominance hierarchy before and after queen removal. Prior to queen removal, dominance rank was negatively correlated with body weight and urinary testosterone and cortisol titres in males and females.Queen removal results in social instability and aggression between high ranking individuals. Dominance rank appears to be a good predictor of reproductive status:queens are the highest ranking colony females and are succeeded by the next highest ranking females. The intense dominance–related aggression that accompanies reproductive succession in naked mole–rats provides empirical support for optimal skew theory.

Dominance and queen succession in captive colonies of the eusocial naked mole-rat, Heterocephalus glaber.

To investigate the endocrine cause of reproductive suppression in nonbreeding female naked mole-rats, animals from 35 colonies were studied in captivity. Urinary and plasma progesterone concentrations were elevated in pregnant females (urine: 10.0-148.4 ng/mg Cr, 27 samples from 8 females; plasma: 3.6-30.0 ng/ml, 5 samples from 5 females; Days 21-40 of pregnancy) and cyclic breeding females (urine: 0.5-97.8 ng/mg Cr, 146 samples from 7 females; plasma: less than 1.0-35.4 ng/ml, 25 samples from 7 females). The latter group showed cyclic patterns of urinary progesterone, indicating a mean ovarian cycle length of 34.4 +/- 1.6 days (mean +/- s.e.m.) with a follicular phase of 6.0 +/- 0.6 days and a luteal phase of 27.5 +/- 1.3 days (19 cycles from 9 breeding females). In non-breeding females urinary and plasma progesterone values were undetectable (urine: less than 0.5 ng/mg Cr, 232 samples from 64 females; plasma: less than 1.0 ng/ml, 7 samples from 6 females). Breeding females had higher (P less than 0.001) plasma LH concentrations (3.0 +/- 0.2 mi.u./ml, 73 samples from 24 females) than did non-breeding females (1.6 +/- 0.1 mi.u./ml, 57 samples from 44 females). Urinary and plasma progesterone concentrations in non-breeding females from wild colonies situated near Mtito Andei, Kenya, were either below the assay sensitivity limit (urine: less than 0.5 ng/mg Cr, 11 females from 2 colonies; plasma: less than 1.0 ng/ml, 25 females from 4 colonies), or very low (plasma: 1.6 +/- 0.6 ng/ml, 15 females from 4 colonies). In captivity, non-breeding females removed from their colonies (i.e. the dominant breeding female) and either paired directly with a non-breeding male (N = 2), or removed and housed singly for 6 weeks before pairing with a non-breeding male (N = 5) may develop a perforate vagina for the first time in as little as 7 days. Urinary progesterone concentrations rose above 2.0 ng/mg Cr (indicative of a luteal phase) for the first time 8.0 +/- 1.9 days after being separated. These results suggest that ovulation is suppressed in subordinate non-breeding female naked mole-rats in captive and wild colonies, and show that plasma LH concentrations are significantly lower in these non-breeding females. This reproductive block in non-breeding females is readily reversible if the social factors suppressing reproduction are removed.

/pdf/social-suppression-of-ovarian-cyclicity-in-captive-and-wild-4kt6vvqe44.pdf

Chris G. Faulkes

Papers

African Mole-Rats: Ecology and Eusociality

A dispersive morph in the naked mole-rat.

Ecological constraints drive social evolution in the African mole-rats.

Dominance and queen succession in captive colonies of the eusocial naked mole-rat, Heterocephalus glaber.

Social suppression of ovarian cyclicity in captive and wild colonies of naked mole-rats, Heterocephalus glaber