Molecular and morphometric variation in European populations of the articulate brachiopod <i>Terebeatulina retusa</i>

Molecular and morphometric variation within and between population samples of the articulate brachiopod &lt;i&gt;Terebratulina&lt;/i&gt; spp., collected in 1985-1987 from a Norwegian fjord, sea lochs and costal sites in western Scotland, the southern English Channel (Brittany) and the western Mediterranean, were measured by the analysis of variation in the lengths of mitochondrial DNA (mtDNA) fragments produced by digestion with nine restriction endonucleases and by multivariate statistical analysis of six selected morphometric parameters. Nucleotide difference within each population sample was high. Nucleotide difference between population samples from the Scottish sites, both those that are tidally contiguous and those that appear to be geographically isolated, were not significantly different from zero. Nucleotide differences between the populations samples from Norway, Brittany, Scotland and the western Mediterranean were also very low. Morphometric analysis confirmed the absence of substantial differentiation

Estimating the duration of speciation from phylogenies

Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.</p

Disparate dispersal limitation in Geomalacus slugs unveiled by the shape and slope of the genetic–spatial distance relationship

Long‐term dispersal ability is a key species’ trait constraining species ranges and thus large‐scale biodiversity patterns. Here we infer the long‐term dispersal abilities of three Geomalacus (Gastropoda, Pulmonata) species from their range‐wide genetic–spatial distance relationships. This approach follows recent advances in statistical modelling of the analogous pattern at the community level: the distance decay in assemblage similarity. While linear relationships are expected for species with high long‐term dispersal abilities, asymptotic relationships are expected for those with more restricted mobility. We evaluated three functional forms (linear, negative exponential and power‐law) for the relationship between genetic distance (computed from mitochondrial cox1 sequences, n = 701) and spatial distance. Range fragmentation at present time and at the Last Glacial Maximum was also estimated based on the projection of climatic niches. The power‐law function best fit the relationship between genetic and spatial distances, suggesting strong dispersal limitation and long‐term population isolation in all three species. However, the differences in slope and explained variance pointed to disparities in dispersal ability among these weak dispersers. Phylogeographic patterns of Geomalacus species are thus largely driven by the same major process (i.e. dispersal limitation), operating at different strengths. This strong dispersal limitation results in geographic clustering of genetic diversity that makes these species highly vulnerable to genetic erosion due to climate changThe authors were supported by the Spanish Ministry of Economy and Competitiveness and the European Regional Development Fund (ERDF) through grant CGL2016‐76637‐P and fellowship IJCI‐2014‐20881 to CG‐RS

Genetic Subdivision and Variation in Selfing Rates Among Central American Populations of the Mangrove Rivulus, Kryptolebias marmoratus.

We used 32 polymorphic microsatellite loci to investigate how a mixed-mating system affects population genetic structure in Central American populations (N = 243 individuals) of the killifish Kryptolebias marmoratus (mangrove rivulus), 1 of 2 of the world's only known self-fertilizing vertebrates. Results were also compared with previous microsatellite surveys of Floridian populations of this species. For several populations in Belize and Honduras, population structure and genetic differentiation were pronounced and higher than in Florida, even though the opposite trend was expected because populations in the latter region were presumably smaller and highly selfing. The deduced frequency of selfing (s) ranged from s = 0.39-0.99 across geographic locales in Central America. This heterogeneity in selfing rates was in stark contrast to Florida, where s &gt; 0.9. The frequency of outcrossing in a population (t = 1 - s) was tenuously correlated with local frequencies of males, suggesting that males are one of many factors influencing outcrossing. Observed distributions of individual heterozygosity showed good agreement with expected distributions under an equilibrium mixed-mating model, indicating that rates of selfing remained relatively constant over many generations. Overall, our results demonstrate the profound consequences of a mixed-mating system for the genetic architecture of a hermaphroditic vertebrate

The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography ofHyla annectanspopulations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32-5.23 million years ago (Ma), a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.Peer reviewe

Microsatellite documentation of male-mediated outcrossing between inbred laboratory strains of the self-fertilizing mangrove killifish (Kryptolebias marmoratus

Abstract Primers for 36 microsatellite loci were developed and employed to characterize genetic stocks and detect possible outcrossing between highly inbred laboratory strainsof the self-fertilizing mangrove killifish, Kryptolebias marmoratus. From attempted crosses involving hermaphrodites from particular geographic strains and gonochoristic males from others, 2 among a total of 32 surveyed progenies (6.2%) displayed multilocus heterozygosity clearly indicative of interstrain gametic syngamy. One of these outcross hybrids was allowed to resume self-fertilization, and microsatellite assays of progeny showed that heterozygosity decreased by approximately 50% after one generation, as expected. Although populations of K. marmoratus consist mostly of synchronous hermaphrodites with efficient mechanisms of internal self-fertilization, these laboratory findings experimentally confirm that conspecific males can mediate occasional outcross events and that this process can release extensive genic heterozygosity. The mangrovekillifish,Kryptolebias(formerlyRivulus)marmoratus, is the only vertebrate species known to reproduce uniparentally by internal self-fertilization Earlier molecular techniques including multilocus DNA fingerprinting have revealed extensive genetic variation in some natural populations of K. marmoratus Materials and Methods Microsatellite Development To enrich for microsatellites in a genomic library for K. marmoratus, we employed a modified version of a hybridization The hybridization solution was mixed with magnetic streptavidin beads (Invitrogen, Carlsbad, CA), and hybridized fragments were captured on a magnetic block. Enriched DNA, recovered by precipitation, was polymerase chain reaction (PCR) amplified (25 ll total reaction volume) under the following conditions: 10 mM Tris-HCl pH 9.0, 50 mM KCl, 0.1% Triton X-100, 2.0 mM MgCl 2 , 25.0 lg/ml bovine serum albumin, 0.2 mM each dNTP, 0.5 lM SuperSNX24 forward primer, and 0.5 units Taq DNA Polymerase (Promega, Madison, WI). The PCR product was ligated into a PCR 2.1-TOPO vector and transformed into One Shot Top10 Chemically Competent Escherichia coli cells. Positive colonies were screened for b-galactosidase activity using materials in the TOPO TA cloning kit (Invitrogen; Carlsbad, CA). Insert sizes were verified from positive colonies by PCR amplification with the M13 forward (À20) and reverse (À27) primers (0.5 lM final concentration). Inserts !500 bp were purified using ExoSAP-IT (United States Biochemicals, Cleveland, OH) and sequenced with Big Dye chemistry (version 3.1, Applied Biosystems, Foster City, CA) using M13 forward or reverse primer on an ABI 3100 Genetic Analyzer equipped with 80-cm capillaries. Sequences were edited using Sequencher version 4.1.4 (Gene Codes Corporation, Ann Arbor, MI), and primers flanking microsatellite regions were developed using OligoAnalyzer 3.0 (Integrated DNA Technologies, Coralville, IA; http://www. idtdna.com/Scitools/Applications/Primerquest/). Primers were tested by amplifying genomic DNA from adult K. marmoratus specimens in laboratory strains initiated many generations ago from single hermaphroditic specimens from Florida, Belize, or Honduras. PCR conditions were optimized for each primer pair, and one primer from each pair was labeled at the 5#-end in either of 2 ways: directly with a 6-FAM or HEX fluorophore (Integrated DNA Technologies) or by attaching a reverse tag (5#-GGAAACAGCTATGACCATG-3#) for tailed PCR with an M13 primer labeled with a 6-FAM, HEX, or NED (Applied Biosystems) fluorophore. The 36 sequences from which primers were developed to amplify microsatellite loci were deposited to GenBank (accession numbers DQ335412-DQ335447). Laboratory Crosses Crossing experiments involved highly inbred laboratory lines each propagated generation after generation by a single selffertilizing hermaphrodite (herm) and each tracing back to a single wild herm originally collected at Utila Island, Honduras (strains Hon2 and Hon7), Belize (Bel50.91), Florida&apos;s Everglades National Park (ENP12), or Brevard County, Florida (CCHA). Each attempted cross involved placing an old (nearly senescent) herm with a secondary male in a small culture dish containing 13% saltwater solution DNA Extractions High molecular weight genomic DNA samples were isolated using a standard guanidinium isothiocyanate (GIT) chaotropic salt procedure Genotypic Assays Amplifications of microsatellite loci with fluorescently labeled PCR primers were performed in a 12.5-ll reaction volume containing 1 ll of purified genomic DNA, PCR Master Mix (Promega), and 0.5 lM of both forward and reverse primers. Tailed PCRs were performed in a 10-ll volume containing 1 ll of purified genomic DNA, 10 mM Tris-HCl pH 9.0, 50 mM KCl, 0.1% Triton X-100, 1.5 mM MgCl 2 , 25.0 lg/ml bovine serum albumin, 0.2 mM each dNTP, 0.25 lM M13-labeled primer, 0.25 lM locus-specific primer, 0.025 lM tailed locus-specific primer, and 0.4 units Taq DNA Polymerase (Promega). PCR products (1.5 ll) were mixed with 2.5 ll deionized formamide, 0.5 ll of either GeneScan-400HD [ROX] or GeneScan-500[ROX] internal lane standard, and 0.5 ll loading dye. Samples were denatured in a 95°C heating block for 3-5 min and chilled on ice before being loaded onto 5% acrylamide gels. Samples were electrophoresed on an ABI 377 DNA Sequencer at 3000 V for 2 h at 55°C. Alleles were sized using the software packages GeneScan version