The genomic signatures of evolutionary stasis.

Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although lineages that appear to exhibit evolutionary stasis are often called living fossils, no single mechanism is thought to be responsible for their slow rates of morphological evolution and low species diversity. Some analyses of molecular evolutionary rates in a handful of living fossil lineages have indicated that these clades exhibit slow rates of genomic change. Here, we investigate mechanisms of evolutionary stasis using a dataset of 1,105 exons for 481 vertebrate species. We demonstrate that two ancient clades of ray-finned fishes classically called living fossils, gars and sturgeons, exhibit the lowest rates of molecular substitution in protein-coding genes among all jawed vertebrates. Comparably low rates of evolution are observed at fourfold degenerate sites in gars and sturgeons, implying a mechanism of stasis decoupled from selection that we speculate is linked to a highly effective DNA repair apparatus. We show that two gar species last sharing common ancestry over 100 million years ago produce morphologically intermediate and fertile hybrids in the wild. This makes gars the oldest naturally hybridizing divergence among eukaryotes and supports a theoretical prediction that slow rates of nucleotide substitution across the genome slow the accumulation of genetic incompatibilities, enabling hybridization across deeply divergent lineages and slowing the rate of speciation over geological timescales. Our results help establish molecular stasis as a barrier to speciation and phenotypic innovation and provide a mechanism to explain the low species diversity in living fossil lineages.

Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii.

The alligator snapping turtle Macrochelys temminckii is a culturally, ecologically, and evolutionary relevant species of conservation concern. In this study, we conducted a genome survey of M. temminckii. Using a low-coverage short read sequencing strategy, this study estimated the genome size, repetitive genome content, annotated and quantified repetitive elements, assembled the 45S rRNA DNA operon, and characterized in detail the mitochondrial genome of M. temminckii. Using a k-mer strategy, the estimated haploid genome size varied between 3.77 and 3.19 Gbp, which is within the range previously reported for other representatives of the family Chelydridae. Repetitive genome content estimates using different k-mers (21 to 51) indicated that more than 75 % of the genome of M. temminckii comprised repetitive elements. Taking into account only annotated repetitive elements, the most common repetitive elements were classified as Class I - Long Interspersed Nuclear Element (LINE) which were more abundant than Class I - Penelope and Class I - Long Terminal Repeat (LTR) Ty3 mobile elements. Less abundant repeat element families in the nuclear genome of M. temminckii included Class I - DIRS mobile elements and Satellite DNA. The nuclear ribosomal operon was partially assembled into three contigs, one encoding the complete ssrRNA gene, a second encoding the complete 5.8S rRNA gene, and a third comprising the full lsrRNA gene. The AT-rich complete mitochondrial genome was 16,570 bp long. These new genomic resources are of utmost importance to aid in the development of conservation plans for this iconic freshwater turtle.

Comparison of Whole Plant and Detached Leaf Screening Techniques for Identifying Anthracnose Resistance in Strawberry Plants.

Anthracnose is a destructive disease of strawberry caused by several Colletotrichum species including C. acutatum, C. fragariae, and C. gloeosporioides. Identification of anthracnose resistant strawberry germplasm has commonly relied on inoculation of whole plants with isolates of these pathogens. In this study, whole plants and detached leaves from 81 germplasm lines were inoculated with a conidial suspension of isolates of C. acutatum, C. fragariae, and C. gloeosporioides, incubated in the dark at 30°C, 100% relative humidity, for 48 h, and assessed for disease severity based on symptoms on inoculated petioles and leaves. The correlation between the disease severity ratings of the whole plants rated 30 days after inoculation and detached leaves rated 5 days after inoculation was determined. Based on leaf symptoms and petiole lesions, the association between the whole plant leaf disease severity rating (DSR) and detached leaf DSR was positive (rp = 0.70), and the association between the whole plant DSR and the detached leaf DSR was also positive (rp = 0.66). Whole plant and detached leaf DSRs were used to assign each germplasm line to a resistance category, and a posthoc Tukey's test showed that the whole plant DSR means and the detached leaf DSR means for each resistance category differed significantly at p < 0.05. This research was used to develop a strawberry detached leaf assay which can reliably and quickly determine the degree of resistance of strawberry germplasm to anthracnose.

Fish faunal provinces of the conterminous United States of America reflect historical geography and familial composition.

Although the conterminous USA has a long history of ichthyological exploration, the description of biogeographical provinces has been ad hoc. In this study we quantitatively determined fish faunal provinces and interpreted them in the context of the geological history of North America. We also evaluated influences of major river basin occupancy and contemporary environmental factors on provincial patterns. Our data set comprised 794 native fishes, which we used to generate a presence and absence matrix for U.S. Geological Survey (USGS) four-digit hydrologic units. Three nested data sets were analysed separately: primary freshwater families, continental freshwater families (including primary and secondary families) and all freshwater families (including primary, secondary and peripheral families). We used clustering analysis to delimit faunal breaks and one-way analysis of similarity (ANOSIM) to determine significance among clusters (i.e. provinces). We used an indicator-species analysis to identify species that contributed most to province delineations and a similarity-percentage (SIMPER) analysis to describe the relative influence of representatives from each category (i.e. primary, secondary, peripheral) on provincial boundaries. Lastly, we used a parsimony redundancy analysis to determine the roles of historical (i.e. major river basin) and contemporary environmental factors in shaping provinces. Analysis of the nested data sets revealed lessening provincial structure with inclusion of more families. There were 10 primary freshwater provinces, 9 continental freshwater provinces and 7 all freshwater provinces. Major basin occupancy, but not contemporary environmental factors, explained substantial variance in faunal similarities among provinces. However, provincial boundaries did not conform strictly to modern river basins, but reflected river-drainage connections of the Quaternary. Provinces represent broad-scale patterns of endemism and provide a starting point for future studies. Relative malleability of province boundaries in the continental interior highlights this region as biogeographically diverse and dynamic. Interior-core provinces of this region (Central Gulf Coastal Plains, Northern Interior) have not been recognized previously and warrant further study.

First record of the invasive Asian fish tapeworm Bothriocephalus acheilognathi in Honduras, Central America.

This paper provides the first report of the invasive Asian fish tapeworm, Bothriocephalus acheilognathi Yamaguti, 1934, in Honduras. The cestode was found in Profundulus portillorum (Cyprinodontiformes: Profundulidae), which represents a new host record, and which is a member of a genus faced with a variety of conservation challenges, now potentially complicated by the presence of this pathogenic cestode. Nearly complete sequence data from the ITS-1 5.8S and ITS-2 regions corroborate the determination based on morphological characteristics. Several species of carp were introduced to Honduras for aquaculture purposes in the early 1980s and the presence of the Asian fish tapeworm in Honduras may be related to these introductions. In addition, this report documents the currently known geographical distribution of this parasite in Central America, first recorded from Panamá and now from Honduras.

Contrasting phylogeographic histories between broadly sympatric topminnows in the Fundulus notatus species complex.

Sympatrically distributed closely related species provide opportunities for studying evolutionary patterns of diversification. Such studies must account for historical contingencies in interpreting contemporary patterns of variation. Topminnows in the Fundulus notatus species complex are distributed sympatrically across much of the southern and Midwestern United States. Throughout most of their ranges F. olivaceus is often found in headwater stream habitats, and F. notatus is more typically distributed along the margins of larger river habitats. However, in some drainages, ecological associations of the respective species are reversed, with F. notatus populations isolated in headwater streams and F. olivaceus in downstream river habitats. Phylogeographic analyses of AFLP marker and multi-locus sequence data detected historical isolation in F. notatus consistent with pre-Pleistocene drainage patterns. Four F. notatus clades corresponded to (i) the Western Gulf Slope, (ii) the southwestern Ouachita Highlands, (iii) the Mobile Basin, and (iv) central Coastal Plain and Mississippi River Basin. In contrast, a relative lack of range-wide geographic structure in F. olivaceus is consistent with recent range expansion over much of the same geographic area. The southwestern Ouachita Highlands and Mobile Basin F. notatus clades corresponded to regions where ecological associations between the two species are reversed, providing evidence of the independent evolution of variation in contemporary habitat associations. Fundulus olivaceus from several drainages demonstrated introgression of mitochondrial DNA from F. notatus, but none of the sites in this study included individuals with hybrid ancestry in their nuclear genome. Phylogenetic analyses that included only nuclear loci supported the reciprocal monophyly of F. notatus, F. olivaceus and a third narrowly endemic species, Fundulus euryzonus, and supported a sister relationship between F. olivaceus and F. euryzonus.

Evolution of a sexually dimorphic trait in a broadly distributed topminnow (Fundulus olivaceus).

Understanding the interaction between sexual and natural selection within variable environments is crucial to our understanding of evolutionary processes. The handicap principle predicts females will prefer males with exaggerated traits provided those traits are indicators of male quality to ensure direct or indirect female benefits. Spatial variability in ecological factors is expected to alter the balance between sexual and natural selection that defines the evolution of such traits. Male and female blackspotted topminnows (Fundulidae: Fundulus olivaceus) display prominent black dorsolateral spots that are variable in number across its broad range. We investigated variability in spot phenotypes at 117 sites across 13 river systems and asked if the trait was sexually dimorphic and positively correlated with measures of fitness (condition and gonadosomatic index [GSI]). Laboratory and mesocosm experiments assessed female mate choice and predation pressure on spot phenotypes. Environmental and community data collected at sampling locations were used to assess predictive models of spot density at the individual, site, and river system level. Greater number of spots was positively correlated with measures of fitness in males. Males with more spots were preferred by females and suffered greater mortality due to predation. Water clarity (turbidity) was the best predictor of spot density on the drainage scale, indicating that sexual and natural selection for the trait may be mediated by local light environments.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009.

This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae.

We report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large-bodied species that has experienced population declines across much of its range. These loci possessed 2-19 alleles and observed heterozygosities of 0-0.974. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management.

Isolation and characterization of microsatellite loci for mountain mullet (Agonostomus monticola).

We report on the isolation of 15 polymorphic microsatellite loci from mountain mullet (Agonostomus monticola). In the two populations sampled, loci exhibited two to 21 alleles and observed heterozygosity values ranged from 0.222 to 1.000. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Although A. monticola is an important subsistence fishery in parts of its range, little is known about its ecology and many populations appear to be experiencing declines. These microsatellite loci should prove useful in the study of population structure of A. monticola and aid in other potential conservation efforts such as the management of hatchery broodstock.