Simulating the extinction of parental lineages from introgressive hybridization: the effects of fitness,initial proportions of parental taxa,and mate choice

Genomic introgression among divergent taxa following human-mediated secondary contact is a growing concern for the management and conservation of aquatic biodiversity. We simulated the composition of taxa following admixture and hybridization by independently altering three variables: (1) initial proportion of parental taxa following secondary contact; (2) fitness gradients among parental and introgressant taxa; and, (3) strength of assortative mating among these taxa. Ultimately, we established that parental taxa will trend toward extinction as introgression proceeds in spite of even a heavy fitness penalty for the hybrids. Also, the number of generations required (rate) to reach an arbitrarily determined threshold of extinction (< 5.0%) was inversely related to the strength of the relative fitness gradients among parental and derivative hybridized lineages. Moreover, the rates of extinction for parental taxa depended on the initial relative proportions in the admixture with rare taxa going extinct more rapidly than abundant taxa. Finally, the strength of assortative mating (as an evolved or reinforced mechanism of pre-mating isolation) will affect the rate of extinction. Introgressive hybridization, therefore, emerges as an important risk to structural biodiversity wherever divergent, yet reproductively compatible, taxa come together naturally or are brought together through human activities.     

Identifying areas of high importance for orchid conservation in east Macedonia (NE Greece)

The establishment of a network of reserves is of fundamental importance to the loss of biodiversity. Seven different area selection methods for the establishment of a reserve network were applied in the present study: (a) 5% cut-off value of the grid cells with the highest species richness or conservation value, (b) complementarity analysis using as criteria species richness or conservation value or rarest species richness, and (c) mixed complementarity analysis using as criteria species richness or conservation value. These methods were applied in the orchid taxa of east Macedonia. The conservation values of taxa were estimated on the basis of regional rarity, broad-scale rarity, and species specialization. The spatial overlap between the resulting networks and the Natura 2000 network of the study area was assessed. Furthermore, the efficiency of the latter network to protect the orchid taxa of the study area was examined. Our results suggest that: (a) a multiscale estimation of rarity is necessary for the unbiased estimation of species conservation values; (b) species specialization adds valuable ecological information to the assessment of taxa conservation values; (c) complementarity and mixed complementarity analyses on species richness or conservation value safeguard all the taxa of the region; (d) complementarity analysis on the basis of the richness of the rarest species safeguards all the rarest taxa, but not the total number of the remaining taxa; (e) the 5% cut-off value on species richness or conservation value fails to protect all the taxa of the region, including a large number of the rarest taxa; and (f) the Natura 2000 network, despite its large coverage in the study area, fails to safeguard all the taxa, including some of the rarest.     

Relative age inference in paleontology

Fossil taxa often occur in a regular vertical order in strata, yet, this regularity does not necessarily imply that the taxa succeeded one another in the same order in time. An argument for the time significance of such a regular pattern is strengthened if (1) the taxa involved were preserved in a wide range of depositional environments, and (2) the Eldredge-Gould model of evolution is correct: by contrast, (3) the areal extent of the pattern and (4) the inferred phylogeny of the taxa involved are not relevant. Paleontologists commonly do conclude that a homotaxial pattern, i.e. a definite orderly succession of fossil taxa, results from the taxa having occurred in essentially the same order in time. The conclusion may be justified as follows: If it is false, there should have been some local areas studied where the taxa (or first and last occurrences of taxa) occur in reverse order, or where two or more allegedly sequential taxa occur together in the same strata. But this is not the case: so the taxa probably succeeded one another in essentially the same order in time. The argument is broadly applicable, yet compelling only if (1) certain constraints involving the prior probability of the conclusion apply, and (2) transgression/regression can be ruled out as a cause of the pattern observed. Subsidiary defenses of the time significance of a homotaxial pattern involve other-group, radiometric, marker-bed, magnetic, seismic, or stable-isotope data. The use of fossils for time correlation of strata does not involve circular reasoning.     

The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study

Many phylogenetic analyses, particularly morphological studies, use higher taxa (e.g., genera, families) rather than species as terminal taxa. This general approach requires dealing with interspecific variation among the species that make up the higher taxon. In this paper, I review different parsimony methods for coding and sampling higher taxa and compare their relative accuracies using computer simulations. Despite their widespread use, methods that involve coding higher taxa as terminals perform poorly in simulations, relative to splitting up the higher taxa and using species as terminals. Among the methods that use higher taxa as terminals, coding a taxon based on the most common condition among the included species (majority or modal coding) is generally more accurate than other coding methods, such as coding taxa as missing or polymorphic. The success of the majority method, and results of further simulations, suggest that in many cases "common equals primitive" within variable taxa, at least for low and intermediate rates of character change. The fixed-only method (excluding variable characters) performs very poorly, a result that is indirectly supported by analyses of published data for squamate reptiles. Sampling only a single species per higher taxon also yields low accuracy under many conditions. Along with recent studies of intraspecific polymorphism, the results of this study show the general importance of (1) including characters despite variation within taxa and (2) using methods that incorporate detailed information on the distribution of states within variable taxa.     

The effect of excluding taxa with low abundances or taxa with small distribution ranges on ecological assessment

The present study aims to investigate whether taxa with a small distribution range or taxa with low abundances indicate specific habitats or a high ecological quality and what the effect is if these taxa are excluded from ecological assessment. We compared autecological features between stream dwelling taxa with a mean abundance >5 individuals per sample and a mean abundance ≤5 individuals per sample as well as between taxa with a small distribution range and taxa with a large distribution range. The number of rare taxa (either with a small distribution range or with low abundances) in a sample was related to the ecological quality classes. To test the effect of exclusion of rare taxa we constructed 8 data sets all including 142 samples of Dutch lowland streams. From each data set we stepwise excluded taxa that had low abundances or taxa that were known to be restricted in their distribution range. With help of the AQEM assessment software we calculated the final ecological quality classes and the metrics that were included in the multimetric for the original data and the 8 selected data sets. Autecological features of the taxa within the different selections showed that taxa with small distribution ranges were often running water taxa, living on stones and gravel and indicating oligosaprobic water conditions in contrast to taxa that had a large distribution range. There were only small differences between taxa with low and high abundances. However, current velocity preference was lower for taxa with abundance ≤5 individuals per sample, saprobic values were higher and scores for typical stream habitats, such as lithal, psammal and akal were lower compared to high abundant taxa. If taxa with low abundances were excluded a higher ecological quality class was achieved in most cases, while excluding taxa with a small distribution range resulted in lower ecological quality classes. In conclusion, excluding taxa with a small distribution range led to worse ecological quality classes because these taxa have special autecological features that often indicate natural streams. On the other hand, excluding taxa with low abundances resulted in higher ecological quality classes because these taxa indicate more disturbed situations and because the number of taxa per sample was strongly reduced. Although the documentation of rare taxa (either with low abundances or with small distribution ranges) is often time and cost-intensive regarding field work, laboratory work, data processing, and analyses, the indicative power of these taxa for natural circumstances is essential and therefore rare taxa should be included in ecological assessment studies.     

Phylogenetic analysis of the Malacostraca (Crustacea)

The Malacostraca comprises about 28 000 species with a broad disparity in morphology, anatomy, embryology, behaviour and ecology. The phylogenetic relationships of the major taxa are still under debate. Is the Leptostraca the sister group of the remaining Malacostraca, or is this taxon more closely related to other Crustacea? Does the Stomatopoda or the Bathynellacea represent the most basal taxon within the remaining taxa? Is the Peracarida monophyletic or are some peracarid taxa more closely related to other ‘caridoid’ taxa? Is the Thermosbaenacea part of the Peracarida or its sister group, and how much support is there for a taxon Amphipoda + Isopoda? To answer these questions a phylogenetic analysis of the Malacostraca combining different phylogenetic approaches was undertaken. In a first step, the monophyly of the Malacostraca including the Leptostraca is shown using the ‘Hennigian approach’. A computer cladistic analysis of the Malacostraca was carried out with NONA and PEE ‐WEE , based on 93 characters from morphology, anatomy and embryology. Nineteen higher malacostracan taxa are included in our analysis. Taxa whose representatives are exclusively fossils were not included. The Leptostraca was used as an operational out‐group. The present analysis supports the basal position of the Stomatopoda. Syncarida and Peracarida (including Thermosbaenacea) are supported as monophyletic, the Eucarida is not. Instead a sister‐group relationship is suggested between Euphausiacea and Peracarida (including Thermosbaenacea), with the Syncarida as the sister group to both taxa. Certain embryonic characters are interpreted as support for the monophyly of the Peracarida (without Thermosbaenacea) because convergences or reversals of these characters seem implausible. Within the Peracarida, the Mysidacea (Lophogastrida + Mysida) represents the sister group to the remaining taxa. A sister‐group relationship between Amphipoda and Isopoda is not supported.     

武夷山稻田生境越冬节肢动物群落的物种组成

2005年12月至2006年3月,采用吸虫器结合人工剥查的方法,对福建省武夷山稻田生境内的越冬节肢动物群落进行系统调查。共采集到节肢动物117种(或类),隶属于3纲13目58科,其中捕食性昆虫15种,蜘蛛23种,寄生性天敌29种,害虫27种,中性昆虫23种。     

稻田周围杂草地生境节肢动物群落的物种组成

2001年5--9月,对福建省古田县中稻田边杂草地生境的节肢动物群落,开展了系统调查,共采集到节肢动物2纲14目112科343种(或类)。其中,天敌184种(包括71种捕食性蜘蛛,31种捕食性昆虫和82种寄生性天敌),害虫52种;中性昆虫107种。     

Some notes on relation between taxon and character in taxonomy (regarding the paper of A.A. Stekol'nikov "A problem of truth...", Zhurnal Obshchei Biologii. 2003.V.64. No 4. P.367-368)

Under brief consideration is the problem of primary or secondary status of the judgments about taxa relative to the judgments about characters in the biological classifications. The following formal definition of taxonomic system (classification) TS is provided: TS = BT[T, C(t), R(t), R(c), R(tc)], where BT is a biological theory constituting content-wise background of the system, T is a set of taxa, C(t) is a set of taxonomic characters, R(t) is a set of relationships among taxa (similarity, kinship, etc.), R(c) is a set of relationships among characters (homology, etc.), and R(tc) is a set of correspondences among taxa and characters. The latter correspondences may be complete or incomplete. At ontological level, there two basical traditions exist in biological systematics regarding R(tc) according to which the biological diversity is patterned either as a set of groups of organisms (taxa) or as a set of their properties (characters). In the first case, taxon is "primary" relative to character (in cladistics); in its opposite, character is "primary" relative to taxon (in scholasticism, classical typology, classical phylogenetics). At epistemological level, incompleteness of the taxon-character correspondence makes classificatory procedure iterative and taxonomic diagnoses context-dependent. The interative nature of classificatory procedure makes the "primary" or "secondary" status of both taxa and characters relative and alternating. This makes it necessary to introduces a kind of uncertainty relation in biological systematics which means impossibility of simultaneous definition of both extensional and intentional parameters of the taxonomic system at each step of classificatory iterations.     

The impact of rare taxa on a fish index of biotic integrity

The index of biotic integrity (IBI) is a commonly used bioassessment tool that integrates abundance and richness measures to assess water quality. In developing IBIs that are both responsive to human disturbance and resistant to natural variability and sampling error, water managers must decide how to weigh information about rare and abundant taxa, which in turn requires an understanding of the sensitivity of indices to rare taxa. Herein, we investigated the influence of rare fish taxa (within the lower 5% of rank abundance curves) on IBI metric and total scores for stream sites in two of Minnesota's major river basins, the St. Croix (n = 293 site visits) and Upper Mississippi (n = 210 site visits). We artificially removed rare taxa from biological samples by (1) separately excluding each individual taxon that fell within the lower 5% of rank abundance curves; (2) simultaneously excluding all taxa that had an abundance of one (singletons) or two (doubletons); and (3) simultaneously excluding all taxa that fell within the lower 5% of rank abundance curves. We then compared IBI metric and total scores before and after removal of rare taxa using the normalized root mean square error (nRMSE) and regression analysis. The difference in IBI metric and total scores increased as more taxa were removed. Moreover, when multiple rare taxa were removed, the nRMSE was related to sample abundance and to total taxa richness, with greater nRMSE observed in samples with a larger number of taxa or sample abundance. Metrics based on relative abundance of fish taxa were less sensitive to the loss of rare taxa, whereas those based on taxa richness were more sensitive, because taxa richness metrics give more weight to rare taxa compared to the relative abundance metrics.     

Vulnerable taxa of European Plecoptera (Insecta) in the context of climate change

We evaluated 516 species and/or subspecies of European stoneflies for vulnerability to climate change according to autoecological data. The variables considered were stream zonation preference, altitude preference, current preference, temperature range preference, endemism and rare species. Presence in ecoregions was used to analyse the vulnerability of taxa in relation to their distribution. We selected the variables that provided information on vulnerability to change in climate. Thus, we chose strictly crenal taxa, high-altitude taxa, rheobionts, cold stenotherm taxa, micro-endemic taxa and rare taxa. Our analysis showed that at least 324 taxa (62.79%) can be included in one or more categories of vulnerability to climate change. Of these, 43 taxa would be included in three or more vulnerability categories, representing the most threatened taxa. The most threatened species and the main factors affecting their distribution are discussed. Endangered potamal species, with populations that have decreased mainly as a consequence of habitat alteration, also could suffer from the effects of climate change. Thus, the total number of taxa at risk is particularly high. Not only are a great diversity of European stoneflies concentrated in the Alps, Pyrenees and Iberian Peninsula, but so are the most vulnerable taxa. These places are likely to be greatly affected by climate change according to climate models. In general, an impoverishment of European Plecoptera taxa will probably occur as a consequence of climate change, and only taxa with wide tolerance ranges will increase in abundance, resulting in lower overall faunal diversity.     

Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods

The use of supraspecific terminal taxa to represent groups of species in phylogenetic analyses can result in changes to inferred relationships as compared to a complete species level analysis. These changes in topology result from interactions among (1) the cladistic status of the supraspecific taxa; (2) the method used to represent the taxa as single terminals, and (3) incongruence in the data set. We examine the effects of using supraspecific terminal taxa using a parallel analysis of hypothetical examples and an actual data matrix for the true seals (Mammalia: Phocidae). Incongruence among characters can produce changes in topology by shifting the ‘balance of power’ among groups of characters when supraspecific taxa are represented as single terminals. In the absence of homoplasy, the correct topology is maintained. Of the three methods for representing supraspecific taxa, the ‘ancestral’ method, which explicidy infers the common ancestor of the group corresponding to the taxon, performed the best, always maintaining the correct topology when monophyletic taxa were represented. This agrees with theoretical predictions. The ‘democratic’ and ‘exemplar’ methods, which represent the higher level taxon through a survey of all or one of its extant constituent species, respectively, were not as effective in maintaining the correct topology. Although both occasionally provided correct answers, their occurrences were largely unpredictable. The success of the exemplar method varies with the species selected. The simultaneous representation of two or more higher level taxa produced interactive effects where the resultant topology included different clades than when the taxa were collapsed individually. Interactive effects occurred with all three methods, albeit to a lesser degree for the ancestral method. Changes in topology were observed regardless of whether the higher group was monophyletic or not, but were more prevalent when it was paraphyletic. Unfortunately, there does not seem to be a reliable way to determine when a paraphyletic group has been included in the analysis (e.g. through bootstrap values or indices measuring homoplasy). The implications of these findings for phylogenetic analyses of molecular data are also discussed.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

Reliability of abundance ratios between aeropalynological taxa as indicators of the climate in France

The abundance ratio between two aeropalynological taxa can sometimes give more reliable information about climate than a single taxon, especially in poorly standardized spectra of sediments, mosses or dusts. The reliabilities of 8385 ratios have been computed from 130 taxa observed in a net of 80 annual standardized aeropalynological spectra measured mostly in France. Ten average climatic factors express cold, heat and rain. The reliability of a pollen ratio is the relative frequency (between 0 and 100%) of the ranks, in the range of the climatic factor, where the ratio is more indicative than its two parent taxa. Only 169 out of the 8,385 ratios have a reliability of 80% or more, with one thousand ratios having a reliability of 50% or more. The most reliable ratios are from the less indicative taxa, whereas ubiquitous taxa give generally unreliable ratios. The accuracy and stability of estimates are approximately the same from the ratios as from the single taxa. The use of ratios foreshadows the use of sociological relations between taxa. Sociological processing will be used to transform the intermittent information about the environment given by the observed abundance of taxa into a gradual information given by their probable abundance.     

Diversity of higher plants in China

The Species Catalogue of China: Volume 1: Plants (SCCP) is a new, comprehensive, hardcopy inventory of Chinese higher plants that combines several datasets and references to recent taxonomic treatments. The database, with all attached additional information, is freely accessible via the internet (http://www.sp2000.org.cn/) and on CD-ROM, and will be updated yearly. It includes bryophytes (157 families, 599 genera, and 3167 specific and infraspecific taxa), lycophytes and ferns (41 families, 181 genera, and 2336 specific and infraspecific taxa), gymnosperms (10 families, 45 genera, and 311 specific and infraspecific taxa), and angiosperms (270 families, 3227 genera, and 35 873 specific and infraspecific taxa); in total 478 families, 4052 genera, and 41 687 specific and infraspecific taxa. Several other important statistics can also be drawn from the database, such as the distribution pattern of the four major groups of higher plants, as well as number of endemic and naturalized or cultivated genera/taxa. Entries in SCCP are also compared with Flora of China, and Flora reipublicae popularis Sinicae at the genus level. The SCCP will not only be a useful reference for floristic or biodiversity studies in China, but will also serve as a key resource to direct action and monitor progress. It is intended to be a useful resource for achieving Target 1 of the Global Strategy for Plant Conservation (GSPC).     

基于底栖生物完整性指数的赣江流域河流健康评价

底栖生物完整性指数(B-IBI)是最为广泛应用的水生态系统健康评价指数之一。根据2009-2010年期间赣江流域60个采样点的底栖动物数据(15个参照点, 45个受损点), 对17个生物参数进行分布范围、判别能力和Pearson相关性分析, 确定了B-IBI指数体系由总分类单元数、甲壳和软体动物分类单元数、甲壳和软体动物%和BI指数构成。采用比值法统一各生物参数量纲, 将各个生物参数分值加和得到B-IBI指数值。根据参照点的B-IBI值的25%分位数值最终确定赣江流域河流健康评价标准。评价结果表明, 赣江流域60个采样点中19个为健康, 19个为亚健康, 14个为一般, 8个较差。综合来看, 赣江流域河流处于健康-亚健康状态: 上游各支流中绵水、贡江、上犹江和桃江为健康状态, 章水、濂水、梅江和平江为较差状态; 中游各支流健康评价结果多为健康-亚健康状态, 而乌江为较差状态; 下游各支流为健康-亚健康状态; 赣江干流上健康评价的结果均为健康。       

Checklist of beetles (Coleoptera) of Canada and Alaska. Second edition

All 8237 species-group taxa of Coleoptera known to occur in Canada and Alaska are recorded by province/territory or state, along with their author(s) and year of publication, in a classification framework. Only presence of taxa in each Canadian province or territory and Alaska is noted. Labrador is considered a distinct geographical entity. Adventive and Holarctic species-group taxa are indicated. References to pertinent identification keys are given under the corresponding supraspecific taxa in the data archive.     

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.