Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems

Arising in the context of biodiversity conservation, the Budgeted Nature Reserve Selection (BNRS) problem is to select, subject to budgetary constraints, a set of regions to conserve so that the phylogenetic diversity (PD) of the set of species contained within those regions is maximized. Here PD is measured across either a single rooted tree or a single unrooted tree. Nevertheless, in both settings, this problem is NP-hard. However, it was recently shown that, for each setting, there is a polynomial-time ${(1-\frac{1}{e})}$ -approximation algorithm for it and that this algorithm is tight. In the first part of the paper, we consider two extensions of BNRS. In the rooted setting we additionally allow for the disappearance of features, for varying survival probabilities across species, and for PD to be measured across multiple trees. In the unrooted setting, we extend to arbitrary split systems. We show that, despite these additional allowances, there remains a polynomial-time ${(1-\frac{1}{e})}$ -approximation algorithm for each extension. In the second part of the paper, we resolve a complexity problem on computing PD across an arbitrary split system left open by Spillner et?al.     

Comparing strategies to preserve evolutionary diversity

The likely future extinction of various species will result in a decline of two quantities: species richness and phylogenetic diversity (PD, or ‘evolutionary history’). Under a simple stochastic model of extinction, we can estimate the expected loss of these quantities under two conservation strategies: An ‘egalitarian’ approach, which reduces the extinction risk of all species, and a ‘targeted’ approach that concentrates conservation effort on the most endangered taxa. For two such strategies that are constrained to experience the same expected loss of species richness, we ask which strategy results in a greater expected loss of PD. Using mathematical analysis and simulation, we describe how the strategy (egalitarian versus targeted) that minimizes the expected loss of PD depends on the distribution of endangered status across the tips of the tree, and the interaction of this status with the branch lengths. For a particular data set consisting of a phylogenetic tree of 62 lemur species, with extinction risks estimated from the IUCN ‘Red List’, we show that both strategies are virtually equivalent, though randomizing these extinction risks across the tip taxa can cause either strategy to outperform the other. In the second part of the paper, we describe an algorithm to determine how extreme the loss of PD for a given decline in species richness can be. We illustrate the use of this algorithm on the lemur tree.     

Resource-aware taxon selection for maximizing phylogenetic diversity

Phylogenetic diversity (PD) is a useful metric for selecting taxa in a range of biological applications, for example, bioconservation and genomics, where the selection is usually constrained by the limited availability of resources. We formalize taxon selection as a conceptually simple optimization problem, aiming to maximize PD subject to resource constraints. This allows us to take into account the different amounts of resources required by the different taxa. Although this is a computationally difficult problem, we present a dynamic programming algorithm that solves it in pseudo-polynomial time. Our algorithm can also solve many instances of the Noah's Ark Problem, a more realistic formulation of taxon selection for biodiversity conservation that allows for taxon-specific extinction risks. These instances extend the set of problems for which solutions are available beyond previously known greedy-tractable cases. Finally, we discuss the relevance of our results to real-life scenarios.     

THE BIOGEOGRAPHY OF SULAWESI REVISITED: IS THERE EVIDENCE FOR A VICARIANT ORIGIN OF TAXA ON WALLACE'S “ANOMALOUS ISLAND”?

Sulawesi, the largest island in the Indonesian biodiversity hotspot region Wallacea, hosts a diverse endemic fauna whose origin has been debated for more than 150 years. We use a comparative approach based on dated phylogenies and geological constraints to test the role of vicariance versus dispersal in the origin of Sulawesi taxa. Most divergence time estimates for the split of Sulawesi lineages from their sister groups postdate relevant tectonic vicariant events, suggesting that the island was predominantly colonized by dispersal. Vicariance cannot be refuted for 20% of the analyzed taxa, though. Although vicariance across Wallace's Line was only supported for one arthropod taxon, divergence time estimates were consistent with a "tectonic dispersal" vicariance hypothesis from the East in three (invertebrate and vertebrate) taxa. Speciation on Sulawesi did not occur before the Miocene, which is consistent with geological evidence for more extensive land on the island from that time. The Pliocene onset of periodic sea-level changes may have played a role in increasing the potential for dispersal to Sulawesi. A more extensive taxon sampling in Wallacea will be crucial for refining our understanding of the region's biogeography and for testing hypotheses on the origin of taxa on its most important island.     

Fission–fusion social systems as a strategy for coping with ecological constraints: a primate case

Fission–fusion social systems, in which members of a social community form frequently changing subgroups, occur in a number of mammalian taxa. Such systems are assumed to be a response to the costs of grouping, but evidence to support this hypothesis is limited. We use a linear programming approach to build a time budget model that predicts the upper bound on group size in order to test the hypothesis that fission–fusion social systems are the outcome of time constraints. Comparative data from 14 wild chimpanzee (Pan spp.) populations are used to derive a set of equations defining the relationship between climatic variables and time budget components, which are then used to calculate the upper limits on group size that can be maintained in different habitats. We validate the model by showing that it correctly predicts the presence/absence of chimpanzees across sub-Saharan Africa and the group sizes observed in natural populations. The model suggests that the costs of travel are limiting for chimpanzees. Chimpanzees can reduce these costs dramatically by fissioning their bonded communities into small foraging parties. If they did not, they would be unable to live in any habitats where they currently occur.     

Phylogenetic inference under the pure drift model

When pairwise genetic distances are used for phylogenetic reconstruction, it is usually assumed that the genetic distance between two taxa contains information about the time after the two taxa diverged. As a result, upon an appropriate transformation if necessary, the distance usually can be fitted to a linear model such that it is expressed as the sum of lengths of all branches that connect the two taxa in a given phylogeny. This kind of distance is referred to as "additive distance." For a phylogenetic tree exclusively driven by random genetic drift, genetic distances related to coancestry coefficients (theta XY) between any two taxa are more suitable. However, these distances are fundamentally different from the additive distance in that coancestry does not contain any information about the time after two taxa split from a common ancestral population; instead, it reflects the time before the two taxa diverged. In other words, the magnitude of theta XY provides information about how long the two taxa share the same evolutionary pathways. The fundamental difference between the two kinds of distances has led to a different algorithm of evaluating phylogenetic trees when theta XY and related distance measures are used. Here we present the new algorithm using the ordinary- least-squares approach but fitting to a different linear model. This treatment allows genetic variation within a taxon to be included in the model. Monte Carlo simulation for a rooted phylogeny of four taxa has verified the efficacy and consistency of the new method. Application of the method to human population was demonstrated.      

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.     

Phylogenetic diversity and the conservation biogeography of African primates

Aim Phylogenetics has an important role in conservation biogeography. However, there are few data on the phylogenetic diversity of African primates. The phylogenetic diversity (PD) of a species is a measure of its taxonomic distinctness and can be estimated by looking at the phylogenetic relationships among taxa. Species‐specific metrics on PD can then be used to determine conservation priorities at various biogeographical scales. We used PD metrics to rank 55 African primate species according to their conservation priorities at the country level and within six African biogeographical regions. We also addressed the following question: are there differences in conservation rankings between the IUCN Red List and our PD metrics? Location Africa. Methods We created a consensus phylogeny for all African primate clades based on genetic studies. Analyses of species distributions were determined using presence/absence scores at two levels: country and biogeographical region. A node‐based method that standardizes for widespread taxa and endemicity was used to calculate PD indices. Hierarchical cluster analysis was used to convert one of the standardized, phylogenetic indices into three clusters that could be ranked and compared with the main IUCN conservation rankings of endangered, vulnerable, and lower risk. Results At the country and region levels, the top‐priority species in terms of PD are Pan paniscus, Macaca sylvanus, Arctocebus calabarensis, Gorilla beringei, Arctocebus aureus, Allenopithecus nigroviridis, Gorilla gorilla, Procolobus verus, Cercopithecus solatus, Cercocebus galeritus, Colobus angolensis, Theropithecus gelada, Galagoides zanzibaricus, Galagoides granti, and Procolobus (Piliocolobus) badius. Geographic rankings were highest for the Democratic Republic of the Congo (country level) and Central Africa (region level). Although there were no overall differences between IUCN conservation ranks and the PD rankings, there were significant differences between the two systems for vulnerable and endangered primate taxa. Main conclusions There are few ecological and behavioural data on populations of some of the African primates that represent the highest levels of phylogenetic diversity. Studies of primate taxa with high PD rankings should focus on identifying sites suitable for intensive studies of population densities, feeding ecology, and reproductive behaviour. We suggest that PD metrics can serve as an important, complementary data set in the IUCN ranking system for primates.     

The Composition and Density of Epiphyton on Some Macrophyte Species in the Partly Meromictic Lake Verevi

In this paper, some important problems related to taxonomic resolution in water quality assessment by means of macroinvertebrates are discussed. Most quality indices based on macroinvertebrates only require identification up to genus or family level. Although this can be seen as a practical trade-off between taxonomic precision and time constraints and financial resources, it can result in biased assessment scores for certain stream types. An additional difficulty of identification levels other than species is caused by possible changes in taxonomy over time. A given genus may indeed have been split up into two or more genera or a species could be assigned to a different genus. These changes may alter biotic index values calculated over time, due to a change in number of taxa or replacement of one taxon by another one having a different tolerance class. An additional problem is caused by the invasion of exotic species. The genus Corbicula for instance is currently invading Belgian watercourses in increasing numbers. Since no Belgian Biotic Index (BBI) tolerance class is defined for Corbicula, this may cause inconsistencies in index calculations as well. In order to eliminate these, a semi-fixed taxa list, including a tolerance class for each taxon, for BBI calculation is proposed.     

Leave it to the leaves: a molecular phylogenetic study of Malaxideae (Epidendroideae, Orchidaceae)

Nuclear ITS and plastid matK sequences were collected for 71 taxa of Malaxideae (Orchidaceae). Resulting cladograms are highly resolved and well supported by jackknife analyses. These indicate that the traditional classification system of the tribe using characters primarily related to floral morphology does not reflect the evolutionary history of these taxa. Rather, the tribe is split into two major clades: one of terrestrial species and another of epiphytes. Within the epiphytic clade, taxa with laterally compressed leaves (Oberonia) are monophyletic, whereas the remaining taxa (Liparis pro parte) have elongate conduplicate leaves and form a paraphyletic grade of at least two additional monophyletic lineages. Within the terrestrial clade, taxa with plicate leaves (Liparis p.p. and Malaxis p.p.) clearly separate from taxa with conduplicate leaves (Liparis p.p. and Malaxis p.p.). Although further taxon sampling should take place before nomenclature is changed, it seems evident that Malaxideae will need to be divided into at least seven genera. Furthermore, the transition from epiphytic to terrestrial habit is documented to have occurred only once in Malaxideae, and the value of vegetative over reproductive features in classifying some groups of orchids is again demonstrated.     

Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system

In the last decade, greater than expected levels of genetic structure have been reported for many marine taxa with high dispersal capabilities. Although little-studied to date, it is predicted that taxa with poor dispersal abilities would exhibit even more genetic differentiation than high dispersal taxa. These systems may track biogeographical processes better than more dispersive taxa and, more critically, function as the 'lowest common denominators' in MPA design initiatives. We investigate phylogeographical patterns in the poorly dispersing, yet widely distributed Patelloida profunda group and related congeners across the Indo-west Pacific region. One hundred and twenty-five individuals were sequenced for COI mtDNA [593 base pairs (bp)] and 44 individuals were sequenced for 16S mtDNA (539 bp). Identified P. profunda group lineages are highly geographically structured, with 12 reciprocally monophyletic lineages reported from 13 localities. Divergences within Indian and Pacific basins range from d = 0.013 to 0.127 and between basins from d = 0.147 to 0.197. The latter split is ancient (> 15 Myr) and cannot be related to Plio-Pleistocene sea-level fluctuations, characteristic of previously reported divergences in the same region. Juxtaposed against this structure is genetic connectivity between two widely separated P. profunda populations that share a common haplotype (phiST = 0.001). This finding contrasts with previous work in the same geographical region and cautions strongly against single taxon indicators for designing conservation priorities or marine protected areas (MPAs). Historical and/or biological factors may play more significant roles than oceanography alone in determining the genetic structuring of taxa. In light of these findings, we discuss the difficulty in deriving biogeographical process or directionality from phylogenetic trees in dispersal-driven systems. Even with a well-resolved, highly supported topology, many equally parsimonious scenarios are possible.     

Constructing circular phylogenetic networks from weighted quartets using simulated annealing

In this paper, we present a heuristic algorithm based on the simulated annealing, SAQ-Net, as a method for constructing phylogenetic networks from weighted quartets. Similar to QNet algorithm, SAQ-Net constructs a collection of circular weighted splits of the taxa set. This collection is represented by a split network. In order to show that SAQ-Net performs better than QNet, we apply these algorithm to both the simulated and actual data sets containing salmonella, Bees, Primates and Rubber data sets. Then we draw phylogenetic networks corresponding to outputs of these algorithms using SplitsTree4 and compare the results. We find that SAQ-Net produces a better circular ordering and phylogenetic networks than QNet in most cases. SAQ-Net has been implemented in Matlab and is available for download at http://bioinf.cs.ipm.ac.ir/softwares/saq.net.     

Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony

Given a set X of taxa, a phylogenetic X-tree T that is only partially resolved, and a collection of characters on X, we consider the problem of finding a resolution (refinement) of T that minimizes the parsimony score of the given characters. Previous work has shown that this problem has a polynomial time solution provided certain strong constraints are imposed on the input. In this paper we provide a new algorithm for this problem, and show that it is fixed parameter tractable under more general conditions.     

Mandibular gland secretions in alloxystine wasps (Hymenoptera,Cynipoidea, Charipidae): do ecological or phylogenetical constraints influence occurrence or composition?

Mandibular gland secretions were investigated in 28 taxa of alloxystine wasps (17 described and 11 potential, hitherto undescribed species) using GC-MS. In two selected species (Alloxysta pleuralis, A. victrix), the chemical patterns of the mandibular gland secretions remained constant and were not qualitatively influenced by different host systems; however, there was a considerable variation in quantity. A cluster analysis revealed the chemical composition to be independent of two different modes of resource utilisation which are characterized by the presence or absence of ants in the respective host system. These results support the idea of the prevalence of historical (phylogenetic) rather than actual ecological constraints. However, the chemotaxonomic applicability of such data on the subfamily level was limited, although a species status could be confirmed in some questionable taxa. By integrating morphological and biological characters, potential relationships of selected species and a hypothetical phylogenetic frame tree are proposed.     

Analyzing and reconstructing reticulation networks under timing constraints

Reticulation networks are now frequently used to model the history of life for various groups of species whose evolutionary past is likely to include reticulation events such as horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to make it temporal by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm, called TemporalHybrid, for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We further derive two methods to decide whether or not a temporal hybridization network exists for two given trees and illustrate one of the methods on a grass data set.     

云南拉沙山黑白仰鼻猴群体规模对冬春季日移动距离和活动时间分配的影响

生态限制模型(Ecological constraints model)认为随种群规模增加,灵长类种群会增加日移动距离、移动时间和取食时间,减少休息时间.果食性灵长类为取食斑块分布的高质量食物资源(如果实)而存在群内分摊竞争(Within-group scramble competition),很好地验证了生态限制模型...     

The probability of correctly resolving a split as an experimental design criterion in phylogenetics

We illustrate how recently developed large sequence-length approximations to probabilities of correct phylogenetic reconstruction for maximum likelihood estimation can be used to evaluate experimental design strategies. The specific criterion of interest is the probability of correctly resolving an a priori defined split of interest in a phylogenetic tree. Design strategies considered include increased taxon sampling and increasing sequence length. Our analyses of specific examples strongly suggest that it is better to sample taxa that connect as close as possible to the split of interest. Assuming this can be done, these examples suggest it is better to sample additional taxa than to add a comparable number of sites for the existing taxa. If the rates of evolution in the added taxa are slow, it is better to choose taxa connecting to a long edge, but if rates are comparable to a sister lineage, it is not necessarily the best strategy to sample taxa connected to a long edge. We also examined deleting taxa while increasing the number of sites. Although deleting a small number of taxa distant from the split of interest can be beneficial, deleting too many or making poor choices as to what should be deleted can lead to smaller probabilities of correct reconstruction than for the original sequence data.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.