Computing phylogenetic diversity for split systems

In conservation biology it is a central problem to measure, predict, and preserve biodiversity as species face extinction. In 1992 Faith proposed measuring the diversity of a collection of species in terms of their relationships on a phylogenetic tree, and to use this information to identify collections of species with high diversity. Here we are interested in some variants of the resulting optimization problem that arise when considering species whose evolution is better represented by a network rather than a tree. More specifically, we consider the problem of computing phylogenetic diversity relative to a split system on a collection of species of size n. We show that for general split systems this problem is NP-hard. In addition we provide some efficient algorithms for some special classes of split systems, in particular presenting an optimal O(n) time algorithm for phylogenetic trees and an O(n log n + nk) time algorithm for choosing an optimal subset of size k relative to a circular split system.     

The effect of costs associated with toxin production in a competitive system

In this paper, we study a two-species competitive system where both the species produce toxin against each other at some cost to their growth rates. A much wider set of outcomes is possible for our system. These outcomes are important contrasts to competitive exclusion or bistable attractors that are often the outcomes for competitive systems. We show that toxin helps to gain an advantage in competition for toxic species whenever the cost of toxin production remains within some moderate value; otherwise it may result in the extinction of the species itself.     

Isolation and characterisation of microsatellite markers for the Australian monitor lizard,Varanus acanthurus (Squamata: Varanidae) and their utility in other selected varanid species

There have been no molecular genetic examinations of mating systems in the Australian varanid lizards (genus Varanus) despite their high species diversity, the abundance of some species and difficulties with direct observation of behaviourally cryptic species in the field. We developed 10 polymorphic microsatellite loci and assessed their utility in a range of varanid species. Observed heterozygosities in the three species assessed ranged from 30% to 100%. These loci should be useful for investigation of population structure, gene flow and mating systems in Varanus acanthurus, V. baritji and V. tristis and may also be of use in other varanid species.     

Comparison of audio recording system performance for detecting and monitoring songbirds

ABSTRACT Acoustic recording systems are being used more frequently to estimate habitat occupancy or relative abundance, and to monitor population trends over time. A potential concern with digital recording systems is that changes in technology could affect detectability of birds and cause bias in trend estimates based on counts of birds detected. We evaluated several currently available commercial recording systems ranging from low‐cost multipurpose digital recorders to custom‐designed wildlife recorders (US$250–$7000 price range) to examine possible differences among systems in species detection. We made recordings during Breeding Bird Surveys (BBS) counts using several units concurrently, and asked several expert birders to listen to the recordings in a factorial design. We found that birders detected, on average, 10% fewer species on some units compared to others, though there was high variance. Analysis of a subset of recordings, using spectrograms and repeated listening, suggested that ～90% of species on each BBS stop could be clearly detected on all units. The remaining species could be identified on at least one unit, but were hard or impossible to detect on others. We found that the recording unit with the lowest empirical signal‐to‐noise‐ratio (SNR) had the lowest number of birds detected on the BBS recordings, and that frequency‐specific SNR differed among units. Missed detections were likely related to variation in internal noise and frequency‐dependent sensitivity of the units, and were an issue for all systems regardless of price. We caution that researchers using recorders need to consider variation among recording systems in their study design, particularly for long‐term monitoring programs.     

IS FLORAL SPECIALIZATION AN EVOLUTIONARY DEAD‐END? POLLINATION SYSTEM TRANSITIONS IN RUELLIA (ACANTHACEAE)

Pollination systems frequently reflect adaptations to particular groups of pollinators. Such systems are indicative of evolutionary specialization and have been important in angiosperm diversification. We studied the evolution of pollination systems in the large genus Ruellia. Phylogenetic analyses, morphological ordinations, ancestral state reconstructions, and a character mapping simulation were conducted to reveal key patterns in the direction and lability of floral characters associated with pollination. We found significant floral morphological differences among species that were generally associated with different groups of floral visitors. Floral evolution has been highly labile and also directional. Some specialized systems such as hawkmoth or bat pollination are likely evolutionary dead-ends. In contrast, specialized pollination by hummingbirds is clearly not a dead-end. We found evidence for multiple reverse transitions from presumed ancestral hummingbird pollination to more derived bee or insect pollination. These repeated origins of insect pollination from hummingbird-pollinated ancestors have not evolved without historical baggage. Flowers of insect-pollinated species derived from hummingbird-pollinated ancestors are morphologically more similar to hummingbird flowers than they are to other more distantly related insect-pollinated flowers. Finally, some pollinator switches were concomitant with changes in floral morphology that are associated with those pollinators. These observations are consistent with the hypothesis that some transitions have been adaptive in the evolution of Ruellia.     

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models.     

Sperm morphology and the evolution of intracellular sperm–egg interactions

Sperm morphology is incredibly diverse, even among closely related species, yet the coevolution between males and females of fertilization recognition systems is necessary for successful karyogamy (male and female pronuclear fusion). In most species, the entire sperm enters the egg during fertilization so sperm morphological diversity may impact the intracellular sperm–egg interactions necessary for karyogamy. We quantified morphological variation of sperm inside eggs prior to and following karyogamy in several species of Drosophila to understand whether evolution of sperm morphology could influence intracellular sperm–egg interactions (ISEIs). We measured seven parameters that describe ISEIs among species to determine whether these parameters varied both within a species across development and across species at the same developmental stage. We used heterospecific crosses to test the relative role of male origin, female origin, and interaction between the male and female in determining ISEIs. We found that sperm shape changed within a species as development proceeded and, at particular development stages, species varied in some ISEIs. Parental origin had an effect on some ISEIs, with a general trend for a stronger female effect. Overall, our findings identify conserved and variable ISEIs among species and demonstrate the potential to contribute understanding to gamete evolution and development.     

A phylogenetically controlled analysis of the roles of reproductive traits in plant invasions

Reproductive traits are tightly linked to plant fitness and may therefore be mechanisms driving biological invasions, including the greater success of more phylogenetically novel introduced species in some systems. We present a phylogenetic comparative analysis of “Baker’s law’’, that introduced plants with the ability to reproduce autogamous or asexually may be better able to establish on introduction. We gathered data from both published and unpublished sources on pollen limitation of 141 species, including 26 introduced species and 115 native species. Our analysis compared differences in the proportion of autonomous autogamy, asexual reproduction, and pollen limitation among native, introduced noninvasive, and introduced invasive plant species, and included the phylogenetic novelty of the introduced species to the native species in that community. Introduced species were more likely to be autogamous than native species, consistent with Baker’s law. On the other hand, introduced species were less likely to have the ability to reproduce asexually. Further, among species with no autonomous autogamy, pollen limitation was greater for introduced compared to native species. Such a result is consistent with the idea that plants entering a new continent receive lower quality or quantity of services from resident pollinators than species native to that continent. Finally, more phylogenetically novel invasive species had lower pollen limitation than less novel invasive species, potentially because they experience less competition for pollinators. This is the first evidence that enhanced pollination may be one mechanism driving the greater invasiveness of phylogenetically novel introduced species observed in some systems.     

Differences in sperm morphology in foam‐nesting leptodactyline frogs (Anura,Leptodactylidae)

Sperm morphology is diverse among vertebrates and is influenced by the reproductive strategies adopted by species. In anurans, sperm morphology is associated with reproductive modes and mating systems. Here, we describe the sperm morphology of 11 frog species in the genus Leptodactylus and that of Lithodytes lineatus and discuss the relationship between sperm morphology and species' mating systems. We observed two distinct sperm morphotypes among the leptodactyline species, which differed mostly in head morphology. Type I sperm had triangular head, discrete acrosome vesicle with posterior margin not clearly visible; type II sperm had elongated head, clear acrosomal vesicle with posterior margin clearly visible. These sperm types do not seem to be associated with phylogeny; instead, type II sperm was observed in all polyandrous species analysed and in species with evidences of polyandry. Moreover, sperm of all species presented tail with undulating membrane connected to the axial fibre. We suggest that differences in sperm morphology might be associated with sperm competition to what polyandrous species are subjected. However, natural history observations on polyandrous mating in some species presenting type II sperm and phylogenetic comparative studies are need to elucidate the role of mating systems in the evolution of sperm morphology in leptodactylines.     

Co-occurrence of multiple, supposedly incompatible modes of sex determination in a lizard population

Sex is determined genetically in some species (genotypic sex determination, or GSD) and by the environment (environmental sex determination, or ESD) in others. The two systems are generally viewed as incompatible alternatives, but we have found that sex determination in a species of montane lizard ( Bassiana duperreyi , Scincidae) in south-eastern Australia is simultaneously affected by sex chromosomes and incubation temperatures, as well as being related to egg size. This species has strongly heteromorphic sex chromosomes, and yet incubation at thermal regimes characteristic of cool natural nests generates primarily male offspring. We infer that incubation temperatures can over-ride genetically determined sex in this species, providing a unique opportunity to explore these alternative sex-determining systems within a single population.     

Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics

Symbioses include some of the clearest cases of coevolution, but their origin, loss or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling more than 61% of the species. We show that the ant-housing Vachellia (Mimosoideae) clade and its ants co-diversified for the past 5 Ma, with some species additionally colonized by younger plant-nesting ant species, some parasitic. An apparent co-radiation of ants and Tachigali (Caesalpinioideae) was followed by waves of colonization by the same ant clade, and subsequent occupation by a younger ant group. Wide crown and stem age differences between the ant-housing genus Triplaris (Polygonaceae) and its obligate ant inhabitants, and stochastic trait mapping, indicate that its domatium evolved earlier than the ants now occupying it, suggesting previous symbioses that dissolved. Parasitic ant species evolved from generalists, not from mutualists, and are younger than the mutualistic systems they parasitize. Our study illuminates the macroevolutionary assembly of ant/plant symbioses, which has been highly dynamic, even in very specialized systems.     

EVOLUTION OF ALLORECOGNITION IN BOTRYLLID ASCIDIANS INFERRED FROM A MOLECULAR PHYLOGENY

Despite the functional and phyletic ubiquity of highly polymorphic genetic recognition systems, the evolution and maintenance of these remarkable loci remain an empirical and theoretical puzzle. Many clonal invertebrates use polymorphic genetic recognition systems to discriminate kin from unrelated individuals during behavioral interactions that mediate competition for space. Space competition may have been a selective force promoting the evolution of highly polymorphic recognition systems, or preexisting polymorphic loci may have been coopted for the purpose of mediating space competition. Ascidian species in the family Botryllidae have an allorecognition system in which fusion or rejection between neighboring colonies is controlled by allele-sharing at a single, highly polymorphic locus. The behavioral sequence involved in allorecognition varies in a species-specific fashion with some species requiring extensive intercolony tissue integration prior to the allorecognition response, while other species contact opposing colonies at only a few points on the outer surface before resolving space conflicts. Due to an apparent species-specific continuum of behavioral variation in the degree of intercolony tissue integration required for allorecognition, this system lends itself to a phylogenetic analysis of the evolution of an allorecognition system. We constructed a molecular phylogeny of the botryllids based on 18S rDNA sequence and mapped allorecognition behavioral variation onto the phylogeny. Our phylogeny shows the basal allorecognition condition for the group is the most internal form of the recognition reaction. More derived species show progressively more external allorecognition responses, and in some cases loss of some features of internal function. We suggest that external allorecognition appears to be a secondary function of a polymorphic discriminatory system that was already in place due to other selective pressures such as gamete, pathogen, or developmental cell lineage recognition.     

Toward a predictive macrosystems framework for migration ecology

Concern about the sustainability of intercontinental‐scale migration systems grows apace with global change. Traditional organism‐centred approaches to this problem have provided insights at the population level, but not at the systems level. We are sceptical that an accumulation of data from a species‐by‐species approach will yield an understanding of these systems in the near term. As an alternative, we advocate a new research programme that grows from an explicitly system‐based framework that leverages existing Earth observation infrastructure to make inferences directly at the macrosystem level. We illustrate how this approach can be used to generate and test system‐level predictions, using NEXRAD radar data as an example. We urge organismal ecologists to recognize that some of the most urgent migration questions are at the macrosystem scale and that tackling these questions requires an interdisciplinary approach if we are to make progress at a pace that exceeds that of climate change.     

Did pollination shifts drive diversification in southern African Gladiolus? Evaluating the model of pollinator-driven speciation

The pollinator-driven ecological speciation model has frequently been invoked to explain plant richness in biodiversity hotspots. Here, by focusing on Gladiolus (260 species), a flagship example of a clade with diverse pollination biology, we test the hypothesis that high species diversity in southern Africa, one of the world's most floristically rich regions, has primarily been driven by ecological shifts in pollination systems. We use phylogenetic methods to estimate rates of transition between the seven highly specialized pollination strategies in Gladiolus. We find that pollination systems have evolved multiple times and that some pollination strategies arose by a variety of evolutionary pathways. Pollination shifts account for up to one-third of all lineage splitting events in the genus, providing partial support for the pollinator-driven speciation model. Transitions from the ancestral pollination mode to derived systems have also resulted in increased rates of diversification, suggesting that certain pollination systems may speed up speciation processes, independently of pollination shifts per se. This study suggests that frequent pollination shifts have played a role in driving high phenotypic and species diversity but indicates that additional factors need to be invoked to account for the spectacular diversification in southern African Gladiolus.     

Inhomogeneous steady state distributions of species in predator--prey systems. A specific example

We present and study a specific example of emergence of an inhomogeneous steady state distribution in a non- Lotka—Volterra predator-prey model. With the aid of a linear and a non-linear bifurcation analysis, the dependence of this distribution on species mobilities as well as other important model parameters is discussed. It is seen that the behaviour of the resulting colonies of species seems to correctly mimic some of the features of real predator-prey systems.     

Breeding System and pollination of selected plants endemic to Juan Fernandez Islands

We conducted field studies on the Juan Fernández Islands flora on the breeding system of 25 endemic species from 17 families. We recorded data on flower features, pollen and ovule number, pollen/ovule ratio, pollen size, self-compatibility, floral visitors, and pollination. Flowers are mostly hermaphrodite, inconspicuous, small, and green. Six species are dioecious. Over 80% of the cosexual species are self compatible. However, many species are dichogamous (mostly protandrous); thus, even the self-compatible species may require pollen transfer. Selfing through geitonogamy seems to be the most common system, and several species express mixed breeding systems. Floral visitors are uncommon to rare, except for two hummingbird species (one native and one endemic) that visit five species we studied. In more than 300 h of observation of flowers over three field seasons, we detected only 23 native insect visits representing ten species (Diptera, Lepidoptera, and Coleoptera). One species each of an introduced ant and an introduced bee were also observed on some flowers, all near the single human settlement of San Juan Bautista. Wind directly moving pollen, or indirectly via shaking the flowers, is the most important pollen distribution mechanism. The majority of the wind-pollinated species bear some typical anemophilous features, but also others not characteristic of wind pollination, that presumably represent the condition of their biotically pollinated ancestors. Floral features often reflect ancestral reproductive systems, so floral biology studies of oceanic islands in particular must be done with cognizance of presumed ancestral forms, because the observed characters can be misleading.     

An Evaluation of the Contribution of Cultivated Allspice (<Emphasis Type="Italic">Pimenta Dioca</Emphasis>) to Vertebrate Biodiversity Conservation in Nicaragua

Tropical deforestation has emerged as one of the most important conservation challenges of our time, both because of the high species diversity and rates of endemism of tropical forests, and because of the rapid rate at which this process is proceeding. Recent studies indicate that areas of low-intensity agroforestry have similar levels of vertebrate diversity as some primary habitats, leading some researchers and conservationists to conclude that this type of commodity production could contribute to the conservation of biodiversity. We compared the composition of bird, mammal and herpetofaunal communities in primary forest, secondary forest, and pasture—and within the allspice productive systems that have replaced pasture. We found that mammal species richness was higher in primary forest than all other habitats; however for resident and migrant birds, amphibians and reptiles, species richness was similar between primary forest and the other habitats. Despite similarities in overall numbers of species, there were numerous species that were encountered only in primary habitats. We conclude that the cultivation of allspice in a mixed productive system can offset some of the losses to biodiversity; however it should be complemented by the establishment and maintenance of protected areas to accommodate populations of primary forest specialists that are unable to persist in altered habitats.     

Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?

Obligate mutualistic nursery pollination systems between insects and plants have led to substantial codiversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems, pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases, host plants sharing pollinators are allopatric. However, in the case of the species group of Ficus auriculata, forms may co‐occur over large parts of their range. We show here that the species group of F. auriculata is constituted by four well‐defined genetic entities that share pollinators. We detected hybrids in nature mainly when both parental forms were growing nearby. Controlled crosses showed that F1 offspring could be successfully backcrossed. Hence, despite sharing pollinators and despite hybrid viability, the different forms have preserved their genetic and morphological identity. We propose that ecological differentiation among forms coupled with limited overlap of reproductive season has facilitated the maintenance of these interfertile forms. As such, establishment of pollinator host specificity may not be a prerequisite for sympatric diversification in Ficus.     

Relationship between soil microarthropod species diversity and plant growth does not change when the system is disturbed

Soil microarthropods influence vital ecosystem processes, such as decomposition and nutrient mineralisation. There is evidence, however, that proper functioning of ecosystems does not require the presence of all its constituent species, and therefore some species can be regarded as functionally redundant. It has been proposed that species redundancy can act as an insurance against unfavourable conditions, and that functionally redundant species may become important when a system has faced a disturbance (the “insurance hypothesis”).
We conducted a laboratory microcosm experiment with coniferous forest soil and a seedling of silver birch (Betula pendula). A gradient of microarthropod diversity (from one to tens of species of soil mites and Collembola) was created to the systems. We disturbed microcosms with drought to test whether systems with altering microarthropod species richness respond differently to perturbations. Primary production (birch biomass), uptake of nitrogen by the birch seedling, the system's ability to retain nutrients and the structure and biomass of the soil microbial community were analysed.
Primary production and nutrient uptake of the birch seedlings increased slightly with increasing microarthropod species richness but only at the species poor end of the diversity gradient. Loss of nutrients and the biomass and community structure of microbes were unaffected by the microarthropods. The effect of drought on the birch biomass production was independent of the species richness of microarthropods. During the disturbance the biomass of microarthropods declined in diverse systems but not in simple ones. These systems were, however, quite resilient; microarthropod communities recovered quickly after the disturbance. Our results suggest that soil microarthropod species are functionally redundant in respect to plant growth, and that the resistance of a system to and its recovery from a disturbance are only weakly related to the species richness of this fauna.