Descent with modification: critical use of historical evidence for conservation

The clear evidence of the accumulating impacts of anthropogenic actions on the Earth system is driving researchers to look to historical data as a resource for understanding the present and predicting the future. In the conservation science literature, using historical sources usually refers to data mining ‘the past’ using the scientific methods of historical ecology. This paper considers the often overlooked methodological challenges of sourcing and interpreting historical data. A schema is provided for conservation scientists, summarising the kinds of questions and metadata required to work rigorously with historical data. This will improve the accuracy of the data we use to construct trends to inform our understanding of the conservation status of particular species and ecosystems. It will also deepen our understanding of the interplays of factors influencing policy and management in particular social-ecological contexts

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/

Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae)

Coalescent-based algorithms coupled with the access to genome-wide data have become powerful tools forassessing questions on recent or rapid diversification, as well as delineating species boundaries in the absence of reciprocal monophyly. In southern South America, the diversification of Liolaemus lizards during the Pleistocene is well documented and has been attributed to the climatic changes that characterized this recent period of time. Past climatic changes had harsh effects at extreme latitudes, including Patagonia, but habitat changes at intermediate latitudes of South America have also been recorded, including expansion of sand fields over northern Patagonia and Pampas). In this work, we apply a coalescent-based approach to study the diversification of the Liolaemus wiegmannii species complex, a morphologically conservative clade that inhabits sandy soils across northwest and south-central Argentina, and the south shores of Uruguay. Using four standard sequence markers (mitochondrial DNA and three nuclear loci) along with ddRADseq data we inferred species limits and a time calibrated species tree for the L. wiegmannii complex in order to evaluate the influence of Quaternary sand expansion/retraction cycles on diversification. We also evaluated the evolutionary independence of the recently described L. gardeli and inferred its phylogenetic position relative to L. wiegmannii. We find strong evidence for six allopatric candidate species within L. wiegmannii, which diversified during the Pleistocene. The Great Patagonian Glaciation (∼1 million years before present) likely split the species complex into two main groups: one composed of lineages associated with sub-Andean sedimentary formations, and the other mostly related to sand fields in the Pampas and northern Patagonia. We hypothesize that early speciation within L. wiegmannii was influenced by the expansion of sand dunes throughout central Argentina and Pampas. Finally, L. gardeli is supported as a distinct lineage nested within the L. wiegmannii complex.Fil: Villamil, Joaquín. Universidad de la República. Facultad de Ciencias; UruguayFil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Sites, Jack W.. University Brigham Young; Estados UnidosFil: Leaché, Adam D.. University of Washington; Estados UnidosFil: Maneyro, Raúl. Universidad de la República. Facultad de Ciencias; UruguayFil: Camargo Bentaberry, Arley. Universidad de la República; Urugua

Clades and clans: a comparison study of two evolutionary models

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1<k<\kappa(n)$, and lower if $\kappa(n)<k<n$. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.Comment: 21page

Evaluating Promotional Approaches for Citizen Science Biological Recording: Bumblebees as a Group Versus Harmonia axyridis as a Flagship for Ladybirds

Over the past decade, the number of biological records submitted by members of the public have increased dramatically. However, this may result in reduced record quality, depending on how species are promoted in the media. Here we examined the two main promotional approaches for citizen science recording schemes: flagship-species, using one charismatic species as an umbrella for the entire group (here, Harmonia axyridis (Pallas) for Coleoptera: Coccinellidae), and general-group, where the group is promoted as a whole and no particular prominence is given to any one species (here, bumblebees, genus Bombus (Hymenoptera: Apidae)). Of the two approaches, the general-group approach produced data that was not biased towards any one species, but far fewer records per year overall. In contrast, the flagship-species approach generated a much larger annual dataset, but heavily biased towards the flagship itself. Therefore, we recommend that the approach for species promotion is fitted to the result desired

Phylogenetic biodiversity assessment based on systematic nomenclature

Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992) and Phylogenetic Diversity (Faith 1992), and Evolutionary History (Nee & May 1997). These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002), ants from a Florida Transect (Lubertazzi & Tschinkel 2003), New England bog ants (Gotelli & Ellison 2002) and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994). The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set

Preliminary evaluation of the quality of water in the Mierzęcka Struga River by a biological method

River quality assessment upon the basis of aquatic macrofauna incidence is already applied in European Union countries. The EU Water Framework Directive (Directive 2000/60/EC) dated October 23, 2000, lays the member countries under an obligation to carry out the biomonitoring of rivers. River classification applied in Poland since 1991 (Regulation of 1991) until 2004 (Regulation of 2004) is based mainly upon physical-chemical data and bacteriological indicators (Coli titre), as well as upon the measurements of saprobic index of seston. Upon the basis of the measured values, the quality of water was assessed according to three classes of quality. In which particular class the tested water should be included is often decided by an indicator least important from the point of view of its usefulness for given purposes. In the European Union countries biotic indices are commonly used for the assessment of the quality of rivers. They are based mainly upon the analysis of the taxonomic composition of macroinvertebrates. Different geographical rangelands of macroinvertebrate species as well as biotypological diversification among watercourses do not allow the use of one universal biotic index. It is necessary to adjust the indices to the local conditions of particular countries. Fulfilling the river quality assessment criteria consistent with the European Union requirements necessitates the undertaking of research that will allow the appropriate biotic indices to be evaluated. The River Mierzęcka Struga is not exposed to industrial contamination, moreover, in its basin there are 39 lakes including a few large ones that are sinks which neutralize pollutions from cultivated fields. This provides an opportunity to test a particular biotic index for small watercourses in the northwest of Poland. First, we tried to assess the quality of the waters of the Mierzęcka Struga using the Brown and Schroeder (Häffner 1993) method.Jaroslaw Nadobni

Invertebrates Fauna of the Lubiatowskie Lakes in the North-West Part of the Note Primeval Forest

The lakes included in the research are called the Lubiatowskie Lakes and they are as follows: Solecko, Lubiatówko, Łkie, Gostomie, Miel, Piersko, Siwino, Glinki, Zdroje, Solczyk, Kliczyna, Rpino. Most of these lakes are flow lakes. The biggest one is Lubowo (102.5 ha) and Solecko (91 ha). The research was conducted from 2003 to 2004, between May and September. The collected material included 14 species of leeches Hirudinea, 22 species of snails Gaspropoda, and 11 species of bivalves Bivalvia as well as several species of dragonflies and ephemerids, 2 species of sponges and 3 species of the Bryozoa. The remote lakes, screened by woods, are often penetrated by poachers with power-generating machines. As a result, invertebrates have become very sparse there. It is an example of a human activity which decreases biological variety in the lakes we have examinedJaroslaw Nadobni