Phylogeographic lineages and species comparisons in conservation analyses: a case study of california herpetofauna

Many phylogeographic studies have revealed strongly diverged lineages within species that are masked by a lack of congruent morphological differentiation. To assess the extent to which the genetic component of diversity affects conservation assessments, we compared spatial patterns of endemism and conservation value for 22 species of Californian amphibians and reptiles with the 75 phylogeographic lineages that they contain. We used bioclimatic distribution modeling with environmental layers to generate 5-km spatial-resolution maps of predicted distribution for each species and lineage. We found concentrations of lineage breaks across the Central Valley, San Francisco Bay, the Sierra Nevada, and the Tehachapi and Trinity ranges. Subdivision of the ranges of species into phylogeographic units revealed novel areas of endemism. Several areas of very high conservation value for lineages were not evident in the species-level analysis. These observations illustrate the importance of considering multiple levels of biodiversity in conservation assessments.     

Isolation and characterization of microsatellite DNA markers in the rare species barfin flounder (Verasper moseri) and its closely related species spotted halibut (V. variegatus)

Barfin flounder and spotted halibut have been selected in Japan as target species for stock enhancement due to the fact that the number of individuals of these species in the wild has been decreasing in the last three decades. Barfin flounder is now considered to be a rare species as its situation is critical. The first microsatellite DNA markers for barfin flounder and spotted halibut are described in this study. Cross‐amplification of barfin flounder markers was examined in spotted halibut species and vice versa.     

Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes

High quality genome is of great significance for the mining of biological information resources of species. Up to now, the genomic information of several important economic flatfishes has been well explained. All these fishes are eyes on left side-type, and no high-quality genome of eyes on right side-type species has been reported. In this study, we applied a combined strategy involving stLFR and Hi-C technologies to generate sequencing data for constructing the chromosomal genome of Verasper variegates, which belongs to Pleuronectidae with characteristic of eyes on right side. The size of genome of V. variegatus is 556 Mb. More than 97.2% of BUSCO genes were detected, and N50 lengths of the contigs and scaffolds reached 79.8 Kb and 23.8 Mb, respectively, demonstrating the outstanding completeness and sequence continuity of the genome. A total of 22,199 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes could be functionally annotated. Meanwhile, the genomic collinearity, gene family and phylogenetic analyses of similar species in Pleuronectiformes were also investigated and portrayed for metamorphosis and benthic adaptation. Sex related genes mapping has also been achieved at the chromosome level. This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.     

Genetic population structure of three Armillaria species at the landscape scale: a case study from Swiss Pinus mugo forests

Armillaria species are plant pathogens that cause Armillaria root rot and are known to cause mortality of mountain pines (Pinus mugo) in the Swiss National Park in the Central Alps. The identity of isolates and the spatially explicit population structure of the Armillaria species were investigated in a 3.3 km² study area in the Swiss National Park. In total, 242 Armillaria isolates, 205 from wood samples and 37 from epiphytic rhizomorphs, were collected. Species were identified using haploid–diploid pairings and genets were determined using intraspecific somatic incompatibility tests. The population structure differed markedly among the Armillaria species. A. cepistipes and A. borealis mainly occurred as genets of small spatial extent (mean 0.2 ha, and 0.6 ha), whereas A. ostoyae formed significantly larger genets (mean 6.8 ha). The largest A. ostoyae genet extended over approx. 37 ha. Several disease centres associated with Heterobasidion annosum were found to be embedded within large Armillaria genets. The extension of large A. ostoyae genets suggests that forests that occupy the study area have developed in the presence of these Armillaria genets. The finding of large Armillaria genets supports the assumption that large genets occur in areas with cold climate and little precipitation.     

The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex

The sheepshead minnow, Cyprinodon variegatus, is a widespread fish species that typically inhabits coastal tidal marsh and mangrove swamp environments, ranging from Cape Cod, Massaschusetts to northern Mexico and into the Caribbean. This wide range crosses several biogeographic boundaries which are coincident with genetic structuring within numerous species originating in the Pleistocene. In addition, the more northerly reaches of this species range have been further subject to the evolutionary consequences of Pleistocene glaciation due to local extinction and recolonization of formerly glaciated sites. C. variegatus thus provides an excellent vertebrate model system within which to test the extent of genetic differentiation among populations in a dominant coastal ecosystem and examine patterns of historical demography in populations distributed along a latitudinal gradient. Using mitochondrial control region and ND2 sequence data, we discovered monophyletic clades within C. variegatus with divergence times within the Pleistocene, and very low gene flow between most sites. Intraspecific genetic breaks appear to correspond broadly to biogeographic or oceanic boundaries. Pleistocene climate change appears to have had dramatic impacts on the size and distribution of populations within and near the glacial margins, but has also affected populations far from formerly glaciated regions.     

Incorporating evolutionary processes into conservation planning using species distribution data: a case study with the western Mediterranean herpetofauna

Aim To incorporate evolutionary processes into conservation planning using species distribution patterns and environmental gradients as surrogates for genetic diversity. Location Western Mediterranean Basin. Methods Distributions of 154 herpetological species were predicted using maximum entropy models, and groups of significantly co‐occurring species (biotic elements) were identified. Environmental gradients were characterized for the complete area and for the area covered by each biotic element, by performing a principal component analysis on the data matrix composed of nine environmental variables. The first two principal component analysis axes were classified into four categories each, and those categories were combined with each other resulting in an environmental classification with 16 categories. To identify priority conservation areas, biotic elements and environmental categories were used as surrogates for the neutral and adaptive components of genetic diversity, respectively. Priority areas for conservation were identified under three scenarios: (1) setting targets for species only; (2) setting targets for species and for each environmental category of the overall area; and (3) setting targets for each species and for each environmental category within each biotic element. Results Nine biotic elements were identified – four for the amphibians and five for the reptiles. Priority areas identified in the three scenarios were similar in terms of amount of area selected, but exhibited low spatial agreement. Main conclusions Prioritization exercises that integrate surrogates for evolutionary processes can deliver spatial priorities that are fairly different to those where only species representation is considered. While new methods are emerging to incorporate molecular data in conservation prioritization, it is unlikely to be enough data for enough taxa for this to be feasible in many regions. We develop an approach using surrogates for both the neutral and adaptive components of genetic diversity that may enhance biodiversity persistence and representation when molecular data are not available or geographically comprehensive.     

Conservation of rare species with island-like distributions: A case study of Lasthenia conjugens (Asteraceae) using population genetic structure and the distribution of rare markers

Californian vernal pools, a patchy, island-like habitat, are endangered as a result of habitat destruction. Conservation of the remaining vernal pool habitat is essential for the persistence of several endangered species. We present the first study examining DNA-level genetic diversity within and among populations of a vernal pool plant species. We investigated genetic variation across eight populations of the US federally endangered vernal pool endemic Lasthenia conjugens (Asteraceae) using intersimple sequence repeat (ISSR) markers. Genetic diversity within the species was high (Nei's gene diversity estimate was 0.37), with moderate differentiation among populations (Bayesian F _ST analog of 0.124). Using an amova analysis, we found that the majority of the genetic variation (84%) was distributed within populations. There is a significant relationship between geographical distance and pairwise genetic differentiation as measured by the Bayesian estimate θ^B. The alternative hypotheses of historic geological processes within the Central Valley and contemporary gene flow are discussed as explanations of the data. Because of the vulnerability of the populations, we calculated a probability of loss for rare alleles (fragments) in the populations. Calculations show that sampling only one of the eight populations for ex-situ conservation or restoration will capture approximately 54% of the sampled rare fragments. We believe that one of the sampled populations has become extinct since it was sampled. When removing this population from the above-mentioned calculations, sampling one population will capture only 41.3% of the sampled rare fragments. We recommend sampling strategies for future conservation and restoration efforts of L. conjugens.     

Using habitat suitability models to sample rare species in high-altitude ecosystems: a case study with Tibetan argali

Models of the distribution of rare and endangered species are important tools for their monitoring and management. Presence data used to build up distribution models can be based on simple random sampling, but this for patchy distributed species results in small number of presences and therefore low precision. Convenience sampling, either based on easily accessible units or a priori knowledge of the species habitat but with no known probability of sampling each unit, is likely to result in biased estimates. Stratified random sampling, with strata defined using habitat suitability models [estimated in the resource selection functions (RSFs) framework] is a promising approach for improving the precision of model parameters. We used this approach to sample the Tibetan argali (Ovis ammon hodgsoni) in Indian Transhimalaya in order to estimate their distribution and to test if it can lead to a significant reduction in survey effort compared to random sampling. We first used an initial sample of argali feeding sites in 2005 and 2006 based on a priori selected vantage points and survey transects. This initial sample was used to build up an initial distribution model. The spatial predictions based on estimated RSFs were then used to define three strata of the study area. The strata were randomly sampled in 2007. As expected, much more presences per hour were obtained in the high quality strata compared to the low quality strata—1.33 obs/h vs. 0.080/h. Furthermore the best models selected on the basis of the prospective sample differed from those using the first a priori sample, suggesting bias in the initial sampling effort. The method therefore has significant implications for decreasing sampling effort in terms of sampling time in the field, especially when dealing with rare species, and removing initial sampling bias.     

Genetic structure of sibling butterfly species affected by Wolbachia infection sweep: evolutionary and biogeographical implications

It was recently recognized that in Japan, the common yellow butterfly, Eurema hecabe, consists of two sibling species, which have been unnamed yet and tentatively called yellow (Y) type and brown (B) type. We investigated the diversity of nuclear and mitochondrial genes in Japanese populations of Y type and B type of E. hecabe. The phylogeny based on nuclear genes agreed with the distinction between Y type and B type, which had been also supported by a wide array of biological data. However, the phylogeny based on mitochondrial genes did not reflect the distinction. PCR survey of Wolbachia revealed that B-type populations were all infected while Y-type populations contained both infected and uninfected individuals. A single genotype of Wolbachia, which was inferred to be a CI-inducing strain from their wsp gene sequence, was prevalent in these populations. Notably, the mitochondrial phylogeny was in perfect agreement with the pattern of Wolbachia infection, suggesting that the Wolbachia infection had affected the mitochondrial genetic structure of the host insects. Probably, the Wolbachia strain and the associated mitochondrial genomes have been occasionally introduced from B-type populations to Y-type populations through migration and subsequent interspecific hybridization, and CI-driven population sweep has been spreading the Wolbachia strain and the particular mitochondrial haplotypes, which originated from B-type populations, into Y-type populations. On the basis of these results together with the geological and biogeographical knowledge of the Japanese Archipelago, we proposed an evolutionary hypothesis on the invasion and spread of Wolbachia infection in B-type and Y-type of E. hecabe.     

Interdisciplinary modeling: a case study of evolutionary economics

Biologists and economists use models to study complex systems. This similarity between these disciplines has led to an interesting development: the borrowing of various components of model-based theorizing between the two domains. A major recent example of this strategy is economists’ utilization of the resources of evolutionary biology in order to construct models of economic systems. This general strategy has come to be called “evolutionary economics” and has been a source of much debate among economists. Although philosophers have developed literatures on the nature of models and modeling, the unique issues surrounding this kind of interdisciplinary model building have yet to be independently investigated. In this paper, we utilize evolutionary economics as a case study in the investigation of more general issues concerning interdisciplinary modeling. We begin by critiquing the distinctions currently used within the evolutionary economics literature and propose an alternative carving of the conceptual terrain. We then argue that the three types of evolutionary economics we distinguish capture distinctions that will be important whenever resources of model-based theorizing are borrowed across distinct scientific domains. Our analysis of these model-building strategies identifies several of the unique methodological and philosophical issues that confront interdisciplinary modeling.     

Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages

In prokaryotes, lateral gene transfer across chromosomal lineages may be mediated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary forces that may restrict gene exchange remain largely unexplored in native settings. In this study, tests of phylogenetic congruence are employed to explore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of legumes. Rhizobial strains isolated from nodules of several host plant genera were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a portion of the 16S rRNA gene. Molecular phylogenetic analysis shows that each locus generally subdivides strains into the same major groups, which correspond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broad phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricultural populations showing broad transfer of sym loci across divergent chromosomal lineages. A general correspondence of the three rhizobial genera with major legume groups suggests that host plant associations may be important in the differentiation of rhizobial nod and chromosomal loci and may restrict lateral transfer among strains. The second major result is a significant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics. This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproductively isolated" and diverge independently. Differences across rhizobial genera in the specificity of host associations imply that the evolutionary dynamics of the symbiosis vary considerably across lineages in native settings.      

Re-terrestrialization in the phylogeny of epiphytic plant lineages: Microsoroid ferns as a case study

The fern family Polypodiaceae, with over 1600 species, is not only one of the most species-rich families of ferns, but also a major contributor to the vascular epiphytic diversity throughout the tropics. Although the vast majority of species belonging to this family prefer to grow as epiphytes, several species colonize successfully rheophytic, lithophytic, and even terrestrial habitats. Here, we explore the hypothesis that non-epiphytic habitat preferences, including terrestrial growth, evolved secondarily with epiphytes being the plesiomorphic habitat preference. The results of phylogenetic analyses, based on dense taxon sampling and four chloroplast DNA regions, were integrated with divergence time estimates and ancestral character state reconstructions to test these predictions. Both fossils and secondary calibration data were incorporated to obtain divergence time estimations. The results support the prediction of multiple transitions from epiphytic/lithophytic to terrestrial/rheophytic habitats occurring mainly in the Microsoreae lineage. The change in niche preferences coincides with niche colonization opportunities created by climatic fluctuations and geographical changes during the Oligocene and Miocene periods.     

Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

Molecular Biology Reports - A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome...     

Stem cells and lineages of the intestine: a developmental and evolutionary perspective

The intestine consists of epithelial cells that secrete digestive enzymes and mucus (gland cells), absorb food particles (enterocytes), and produce hormones (endocrine cells). Intestinal cells are rapidly turned over and need to be replaced. In cnidarians, mitosis of differentiated intestinal cells accounts for much of the replacement; in addition, migratory, multipotent stem cells (interstitial cells) contribute to the production of intestinal cells. In other phyla, intestinal cell replacement is solely the function of stem cells entering the gut from the outside (such as in case of the neoblasts of platyhelminths) or intestinal stem cells located within the midgut epithelium (as in both vertebrates or arthropods). We will attempt in the following to review important aspects of midgut stem cells in different animal groups: where are they located, what types of lineages do they produce, and how do they develop. We will start out with a comparative survey of midgut cell types found across the animal kingdom; then briefly look at the specification of these cells during embryonic development; and finally focus on the stem cells that regenerate midgut cells during adult life. In a number of model systems, including mouse, zebrafish and Drosophila, the molecular pathways controlling intestinal stem cells proliferation and the specification of intestinal cell types are under intensive investigation. We will highlight findings of the recent literature, focusing on aspects that are shared between the different models and that point at evolutionary ancient mechanisms of intestinal cell formation.     

Isolation and characterization of 31 polymorphic microsatellite markers in barfin flounder (Verasper moseri) and the cross-species amplification in spotted halibut (Verasper variegatus)

The construction of a genetic linkage map and evaluation of population genetic diversity both require large numbers of polymorphic molecular markers. In the present study, we report 31 polymorphic microsatellite markers, of which 28 were isolated from two repeat-enriched libraries constructed from genomic DNA, and three were detected in two genes (MCH-R1 and MCH-R2) of barfin flounder (Verasper moseri). A total of 94 alleles were detected with an average of 3.0 alleles per locus. The number of alleles, observed and expected heterozygosity per locus ranged from two to six, from 0.30 to 1.00 and from 0.33 to 0.78, respectively. Three loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0016) and no significant linkage disequilibrum between pairs of loci was found. Cross-species amplification of these markers was evaluated using the closely related species spotted halibut (Verasper variegatus). This study will potentially be useful for stock management, constructing of a genetic linkage map, mapping economically important quantitative trait loci (QTL), and studying the population genetic diversity of barfin flounder (Verasper moseri).     

Genetic structure of a phytophagous mite species affected by crop practices: the case of Tetranychus urticae in clementine mandarins

Tetranychus urticae Koch is a cosmopolitan mite considered as the most polyphagous species among spider mites. This mite is a key pest of clementine mandarins in Eastern Spain, where Spanish clementine production concentrates. Crop management practices can affect the population dynamics of this mite and, consequently, its impact on the orchard. Microsatellite markers were used to study mite population genetics from two commercial orchards which had been managed differently following Integrated Pest Management (IPM) or Organic Pest Management (OPM) schemes during four consecutive years. A multiplex system including 20 microsatellite loci was designed specifically and allowed an efficient and inexpensive genotyping of individual mites. We found that the IPM population had a stronger fluctuation of population structure and higher genetic diversity compared to OPM population. Thus, our study concludes that crop management has an impact on the population genetics of T. urticae which may be related to the alternation of some acaricides under IPM.     

Genetic structure in a progenetic trematode: signs of cryptic species with contrasting reproductive strategies

Complexes of cryptic species are rapidly being discovered in many parasite taxa, including trematodes. However, after they are found, cryptic species are rarely distinguished from each other with respect to key ecological or life history traits. In this study, we applied an integrative taxonomic approach to the discovery of cryptic species within Stegodexamene anguillae, a facultatively progenetic trematode common throughout New Zealand. The presence of cryptic species was determined by the genetic divergence found in the mitochondrial cytochrome c oxidase I gene, the 16S rRNA gene and the nuclear 28S gene, warranting recognition of two distinct species and indicating a possible third species. Speciation was not associated with geographic distribution or microhabitat within the second intermediate host; however frequency of the progenetic reproductive strategy (and the truncated life cycle associated with it) was significantly greater in one of the lineages. Therefore, two lines of evidence, molecular and ecological, support the distinction between these two species and suggest scenarios for their divergence.