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The microbiome is critical to an organism's phenotype, and its composition is shaped by, and a driver of, eco-evolutionary interactions. We investigated how host ancestry, habitat and diet shape gut microbial composition in a mammalian hybrid zone between Neotoma lepida and N. bryanti that occurs across an ecotone between distinct vegetation communities. We found that habitat is the primary determinant of diet, while host genotype is the primary determinant of the gut microbiome-a finding further supported by intermediate microbiome composition in first-generation hybrids. Despite these distinct primary drivers, microbial richness was correlated with diet richness, and individuals that maintained higher dietary richness had greater gut microbial community stability. Both relationships were stronger in the relative dietary generalist of the two parental species. Our findings show that host ancestry interacts with dietary habits to shape the microbiome, ultimately resulting in the phenotypic plasticity that host-microbial interactions allow.

A population of Vaccinium from San Bruno Mountain in San Mateo County, California has been confused with V. cespitosum Michx. (V. sect. Myrtillus), a species documented from the mountain, since its initial collection in 1961. These plants resemble V. cespitosum and other species in V. sect. Myrtillus in several characters, but differ most notably in their evergreen habit and well developed calyx lobes. The latter characters are shared by V. ovatum Pursh (V. sect. Pyxothamnus), the only other species of Vaccinium known from San Bruno Mountain, suggesting that the population is a hybrid between V. cespitosum and V. ovatum. We used data from gross morphology, leaf anatomy, and DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and plastid matK and ndhF regions to test the hybrid status of this population. Hybrid status is supported by: 1) a plastid sequence profile identical to that of V. cespitosum from San Bruno Mountain and different from the profiles of all other Vaccinium samples in the study, 2) an ITS profile that differs from V. cespitosum from the mountain by only two polymorphic sites, and 3) the possession of gross morphological and anatomical characters that are either shared with one putative parent or the other, or are intermediate between them. Although ITS variation was non-additive and closely matched one of the putative parents, uniparental inheritance has been observed in other hybrids. Two novel gross morphological characters were also observed in the hybrid. The study documents a case of likely intersectional hybridization within Vaccinium, only rarely observed under natural conditions. Vaccinium cespitosum may have been outcompeted by the hybrid to the point of its extirpation from San Bruno Mountain. The population is here newly described as the nothospecies Vaccinium ×brunoense P.W.Fritsch, occurring in an area of only ca. 200 m2 with the number of individuals remaining uncertain because of clonal growth.

Hybrid zones are natural laboratories for investigating the dynamics of gene flow, reproductive isolation, and speciation. A predominant marine hybrid (or suture) zone encompasses Christmas Island (CHR) and Cocos (Keeling) Islands (CKE), where 15 different instances of interbreeding between closely related species from Indian and Pacific Oceans have been documented. Here, we report a case of hybridization between genetically differentiated Pacific and Indian Ocean lineages of the three‐spot dascyllus, Dascyllus trimaculatus (Rüppell, 1829). Field observations indicate there are subtle color differences between Pacific and Indian Ocean lineages. Most importantly, population densities of color morphs and genetic analyses (mitochondrial DNA and SNPs obtained via RADSeq) suggest that the pattern of hybridization within the suture zone is not homogeneous. At CHR, both color morphs were present, mitochondrial haplotypes of both lineages were observed, and SNP analyses revealed both pure and hybrid genotypes. Meanwhile, in CKE, the Indian Ocean color morphs were prevalent, only Indian Ocean mitochondrial haplotypes were observed, and SNP analysis showed hybrid individuals with a large proportion (~80%) of their genotypes assigning to the Indian Ocean lineage. We conclude that CHR populations are currently receiving an influx of individuals from both ocean basins, with a greater influence from the Pacific Ocean. In contrast, geographically isolated CKE populations appear to be self‐recruiting and with more influx of individuals from the Indian Ocean. Our research highlights how patterns of hybridization can be different at scales of hundreds of kilometers, due to geographic isolation and the history of interbreeding between lineages., Here, we report a case of cryptic hybridization between genetically differentiated Pacific and Indian Ocean lineages of the threespot dascyllus, Dascyllus trimaculatus, which overlap in the Christmas–Cocos marine suture zone. Population densities of these lineages and genetic analyses (mitochondrial DNA and SNPs) suggest that the pattern of hybridization within the suture zone is not homogeneous: At Christmas Island, hybridization is ongoing; whereas at Cocos (Keeling) Islands, the lineages underwent past hybridization events that resulted in genetically stable allelic frequencies. We conclude that Cocos Island populations are geographically isolated and are self‐recruiting. In contrast, Christmas populations are currently connected and receiving constant influx from both lineages, with major influence from the Pacific Ocean.

The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservation.

The family Syngnathidae is a large and diverse clade of morphologically unique bony fishes, with 57 genera and 300 described species of seahorses, pipefishes, pipehorses, and seadragons. They primarily inhabit shallow coastal waters in temperate and tropical oceans, and are characterized by a fused jaw, male brooding, and extraordinary crypsis. Phylogenetic relationships within the Syngnathidae remain poorly resolved due to lack of generic taxon sampling, few diagnostic morphological characters, and limited molecular data. The phylogenetic placement of the threatened, commercially exploited seahorses remains a topic of intense interest, with conflicting topologies based on morphology and predominantly mitochondrial genetic data. In this study, we integrate eight nuclear and mitochondrial markers and 17 morphological characters to investigate the phylogenetic structure of the family Syngnathidae at the generic level. We include 91 syngnathid species representing 48 of the 57 recognized genera, all major ocean basins, and a broad array of temperate and tropical habitats including rocky and coral reefs, sand and silt, mangroves, seagrass beds, estuaries, and rivers. Maximum likelihood and Bayesian analyses of 5160bp from eight loci produced high congruence among alternate topologies, defining well-supported and sometimes novel clades. We present a hypothesis that confirms a deep phylogenetic split between lineages with trunk- or tail-brood pouch placement, and provides significant new insights into the morphological evolution and biogeography of this highly derived fish clade. Based on the fundamental division between lineages - the tail brooding "Urophori" and the trunk brooding "Gastrophori" - we propose a revision of Syngnathidae classification into only two subfamilies: the Nerophinae and the Syngnathinae. We find support for distinct principal clades within the trunk-brooders and tail-brooders, the latter of which include seahorses, seadragons, independent lineages of pipehorses, and clades that originated in southern Australia and the Western Atlantic. We suggest the seahorse genus Hippocampus is of Indo-Pacific origin and its sister clade is an unexpected grouping of several morphologically disparate Indo-Pacific genera, including the Pacific pygmy pipehorses. Taxonomic revision is required for multiple genera, particularly to reflect deep evolutionary splits in nominal lineages from the Atlantic versus the Indo-Pacific.

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Ne ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased Ne between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation., Financial support for this work was provided by Instituto Antártico Chileno (INACH RT_12–14), Fondecyt Project 1150517, Genomics Antarctic Biodiversity/Programa de Investigación Asociativa/Comisión Nacional de Investigación Científica y Tecnológica (GAB PIA CONICYT ACT172065), NSF DEB-1441652, French Polar Institute Paul-Emile Victor (IPEV; Progs. 137 and 354), a Lakeside grant from the California Academy of Sciences, and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Brazil and Instituto Nacional de Ciência e Tecnologia - Ecologia, Evolução e Conservação da Biodiversidade (INCT-EECBio) Brazil.

The most ubiquitous, abundant, and invasive turtle on Earth, Trachemys scripta elegans (TSE, “red-eared slider”), is one of four taxa in a clade that is native to the USA and adjacent Mexico (three subspecies of Trachemys scripta plus Trachemys gaigeae). The present range-wide study of this clade is based on 173 known-locality mtDNA sequences combined with ddRAD libraries for 43 samples emphasizing the western part of the range of TSE, its contact with that of T. gaigeae, and anthropogenic hybrids between TSE and T. s. scripta. The data presented here are the first to sample the TSE × T. s. scripta intergrade zone or TSE × T. s. scripta crosses from introduced turtles. In the western part of its range (New Mexico and Texas), most samples of TSE from the Pecos River have mtDNA haplotypes matching T. gaigeae. Structure analysis of SNPs from the ddRAD show evidence of genetic admixture between T. gaigeae and TSE in all included samples from the Rio Grande and Pecos River. These populations also exhibit T. gaigeae-like head stripes, i.e., a postorbital marking that does not reach the eye. The genetic and morphological data are thereby reconciled, as both suggest that these TSE are intergrades. We recommend that these populations continue to be considered TSE, despite the admixture with T. gaigeae. In the Eastern United States, some samples of the morphologically intermediate subspecies T. s. troostii are not genetically distinct from TSE and some samples share morphological characters and genetic affinities with T. s. scripta. Based on these observations we conclude that the taxon T. s. troostii represents intergrades between TSE and T. s. scripta and should not be considered a valid taxon. Near the already established part of the intergrade zone between TSE and T. s. scripta, TSE mtDNA haplotypes have naturally introgressed into typical-looking samples of T. s. scripta in Georgia. Hybrids between introduced TSE and T. s. scripta are also confirmed deeper within the natural range of T. s. scripta in South Carolina and Virginia. Given the examples of feral hybrids deep within its range shown here and elsewhere, the threat of genetic pollution of T. s. scripta by feral TSE is established.

Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.

In Styrax (Ericales: Styracaceae), gynodioecy is known or likely in ten species. A previous morphological analysis of the genus placed these species into a single highly derived clade within S. series Valvatae. In contrast, DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region yielded two distinct gynodioecious clades within the series, one (South American species) as sister to the rest of S. series Valvatae, the other (S. obtusifolius only; Cuba) as phylogenetically nested within a clade of otherwise hermaphroditic species. Here we test these contrasting phylogenetic placements with analyses that include the plastid ndhF-rpl32-trnL, trnL-trnF, trnS-trnG, and trnV-ndhC genic regions in addition to ITS. Results strongly corroborate the phylogenetic positions of the two gynodioecious clades based on ITS data alone. Clade-specific ITS-plastid phylogenetic discordance provides evidence for hybridization and suggests a pattern of reticulate evolution among some of the s...

The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.

Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses.

The shrew Crocidura thomensis is a little-known species endemic to São Tomé Island. We review its distribution, ecology and conservation status based on nine published and 23 new records. The species has a wide distribution across São Tomé, preferring rugged forested areas with high rainfall. The location of new records coincides with that of historical records but the proportion of records in plantations has declined, possibly as a result of agricultural intensification, increased use of pesticides, and presence of exotic species. The shrew is restricted to a single island, its extent of occurrence is 2 and its habitat is declining in extent and quality, and thus its categorization as Endangered on the IUCN Red List remains appropriate. It is important to gain a better knowledge of population trends, ecological preferences and sensitivity to potential threats, but the effective protection of São Tomé Obô Natural Park and surrounding forests is the most important measure to ensure the long-term survival of this mammal.

Two new species of Conopea (Say 1822) are described from the Gulf of Guinea: Conopea saotomensis sp. n. and Conopea fidelis sp. n. These two new species were collected from the historically isolated volcanic islands of São Tomé and Príncipe. The relationship between Conopea saotomensis sp. n., Conopea fidelis sp. n. and two other Atlantic barnacle species, Conopea calceola (Ellis 1758) and Conopea galeata (Linnaeus 1771), is examined. The methods employed are the construction of a molecular phylogeny using mitochondrial COI and nuclear H3 gene sequence data along with morphological comparisons of calcareous and cuticular body parts. It is found that Conopea saotomensis sp. n., Conopea fidelis sp. n. and Conopea calceola are most closely related to each other but the relationship among them is unresolved. Gorgonian hosts are identified. Preliminary observations show species level host specificity for C. fidelis sp. n.

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Alegre, RS, Brazil Royal Museum Cent Africa, Tervuren, Belgium Univ Nacl Autonoma Mexico, Mexico City, DF, Mexico Univ Innsbruck, Inst Ecol, Innsbruck, Austria Hasselt Univ, Hasselt, Belgium Univ Fed Pernambuco, Recife, PE, Brazil Univ Fed Espirito Santo, Vitoria, ES, Brazil Univ Nacl Misiones, Felix De Azara, Argentina Albany Museum, Grahamstown, South Africa Natl Museum, Bloemfontein, South Africa Senckenberg Nat Hist Sammlungen, Dresden, Germany Univ Estadual Paulista, Botucatu, SP, Brazil Stephen F Austin State Univ, Nacogdoches, TX 75962 USA Landesmuseum, Leonding, Austria Univ Camerino, Camerino, Italy Univ Fed ABC, Sao Bernardo, Brazil Univ Estadual Londrina, Museu Zool, Londrina, Parana, Brazil Senckenberg Res Inst, Frankfurt, Germany Museo Civ Storia Nat, Carmagnola, Italy Polskiej Akad Nauk, Muzeum & Inst Zool, Warsaw, Poland Museo Civ Storia Nat, Genoa, Italy Russian Acad Sci, Inst Zool, St Petersburg, Russia Univ Estadual Paulista, Sao Vicente, Brazil Sorbonne Univ, ISYEB, Museum Natl Hist Nat, Paris, France Port Elizabeth Museum, Port Elizabeth, South Africa Sam Noble Museum, Norman, OK USA Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA North West Univ, Potchefstroom, South Africa Museu Nacl, Rio De Janeiro, Brazil Nat Hist Museum, Basel, Switzerland Senckenberg Nat Kundemuseum, Gorlitz, Germany North Carolina Museum Nat Sci, Raleigh, NC USA Univ Rennes 1, Rennes, France Univ Sao Paulo, Museu Zool, Sao Paulo, SP, Brazil Amer Museum Nat Hist, New York, NY 10024 USA Univ Huddersfield, Huddersfield, W Yorkshire, England North Dakota State Univ, Fargo, ND USA Univ Sao Paulo, Sao Paulo, SP, Brazil Fac Sci Sfax, Sfax, Tunisia DPTC PC, Manaus, Amazonas, Brazil Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 USA Zool Survey India, Kolkata, India Univ Tennessee, Chattanooga, TN USA Ohio State Univ, Columbus, OH 43210 USA Univ Luterana Brasil, Museu Ciencias Nat, Canoas, Brazil Univ Firenze, Florence, Italy Univ Ovidius Constanta, Constanta, Romania Univ Mississippi, Oxford, MS USA Royal Belgian Inst Nat Sci, Brussels, Belgium Univ New Mexico, Albuquerque, NM 87131 USA Inst Nacl de Pesquisas da Amazonia, Manaus, Amazonas, Brazil Univ Stellenbosch, Matieland, South Africa Univ Fed Minas Gerais, Belo Horizonte, MG, Brazil CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal Museum Hist Nat, Geneva, Switzerland Univ Fed Mato Grosso, Cuiaba, Brazil Univ Austral Chile, Valdivia, Chile Univ Malaysia, Sarawak, Malaysia Indian Inst Sci, Bangalore, Karnataka, India Scottish Assoc Marine Sci, Oban, Argyll, Scotland Sam Houston State Univ, Huntsville, TX 77340 USA Museo Nacl Ciencias Nat, Madrid, Spain Sorbonne Univ, CR2P, Museum Natl Hist Nat, Paris, France Drexel Univ, Acad Nat Sci, Philadelphia, PA 19104 USA Univ Richmond, Richmond, VA 23173 USA Ctr Pesquisas Cacau, Itabuna, Brazil Univ Torino, Turin, Italy Soc Hist Nat Alcide dOrbigny, Aubiere, France Wolfden Sci Consulting, Murcia, Spain Univ Fed Rio de Janeiro, Macae, Brazil Univ Tennessee, Knoxville, TN USA Inst Humboldt, Villa De Leyva, Colombia Escuela Politec Nacl, Quito, Ecuador Calif Acad Sci, San Francisco, CA 94118 USA Museum Dept Hist Nat Var, Toulon, France Nat Environm & Wildlife Soc, Angul, India Univ Kansas, Lawrence, KS 66045 USA Kyoto Univ, Kyoto, Japan Consejo Nacl Invest Cient & Tecn, Museo Argentino Ciencias Nat Bernardino Rivadavia, Buenos Aires, DF, Argentina Univ Fed Paraiba, Joao Pessoa, Paraiba, Brazil Univ Fed Parana, Curitiba, Parana, Brazil Univ Fed Rio de Janeiro, Rio De Janeiro, Brazil Nat Hist Museum Narodini Museum, Prague, Czech Republic Nat Hist Museum Zimbabwe, Bulawayo, Zimbabwe Ateneo Manila Univ, Quezon City, Philippines Pontificia Univ Javeriana, Bogota, Colombia RACINE, St Maugan, France Univ Paris 06, Sorbonne Univ Paris, ISYEB, Paris, France Ocean Univ China, Qingdao, Peoples R China Museo Nacl Hist Nat Paraguay, San Lorenzo, Paraguay Univ Carabobo, Valencia, Venezuela Natl Ctr Biol Sci, 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Jr Coll, Santa Rosa, CA USA George Washington Univ, Washington, DC 20037 USA Inst Teknol Bandung, Bandung, Indonesia Earlham Coll, Richmond, IN USA Senckenberg Forschungsinst & Nat Museum, Frankfurt, Germany Univ Estadual Londrina, Londrina, Parana, Brazil Univ Koblenz Landau, Koblenz, Germany Nat Hist Museum, London, England Ditsong Natl Museum Nat Hist, Pretoria, South Africa Bombay Nat Hist Soc, Bombay, Maharashtra, India Philipps Univ Marburg, Marburg, Germany Hess Landesmuseum, Darmstadt, Germany Smithsonian Conservat Biol Inst, Washington, DC USA Univ Pannonia, Keszthely, Hungary Staatliches Museum Nat Kunde, Stuttgart, Germany UFT, Tocantins, Portugal Museum Nat Kunde, Berlin, Germany Nat Hist Riksmuseet, Stockholm, Sweden Hikarigaoka, Munakata, Japan Inst Agr & Environm Sci, Tartu, Estonia Univ Los Andes, Merida, Venezuela Bat Jungle, Monteverde, Costa Rica Texas A&M Univ, College Stn, TX USA Yale Univ, New Haven, CT USA Univ Estadual Paulista, Sao Jose Do Rio Preto, Brazil Museo Nacl Hist Nat, Montevideo, Uruguay Consejo Nacl Invest Cient & Tecn, Fdn Miguel Lillo, San Miguel De Tucuman, Argentina Roger Tory Peterson Inst Nat Hist, Jamestown, VA USA Univ Fed Reconcavo Bahia, Cruz Das Almas, Brazil South China Normal Univ, Guangzhou 510631, Guangdong, Peoples R China Museu Ciencias Tecnol PUCRS, Porto Alegre, RS, Brazil Univ Fed Tocantins, Porto Nacl, Brazil Univ Toronto, Scarborough, ON, Canada Univ Nacl Colombia, Inst Ciencias Nat, Bogota, Colombia Natl Museum Philippines, Manila, Philippines NOVA Univ Lisbon, Caparica, Portugal Royal Saskatchewan Museum, Regina, SK, Canada Deutsch Zentrum Marine Biodiversitatsforsch, Hamburg, Germany Ctr Invest Biol Noroeste, La Paz, Mexico Naturalis Biodivers Ctr, Leiden, Netherlands Univ Douala, Douala, Cameroon Vet & Farmaceut Univ Brno, Brno, Czech Republic Univ Swaziland, Kwaluseni, Eswatini Fundacao Oswaldo Cruz, Rio De Janeiro, Brazil Univ Claude Bernard, Lyon, France Museum Vertebrate Zool, Berkeley, CA USA Smithsonian Inst, Washington, DC 20560 USA Nat Hist Museum & Inst, Chiba, Japan Senckenberg Biodiversitat & Klima Forschunsgzentr, Frankfurt, Germany Marquette Univ, Milwaukee, WI 53233 USA Univ Firenze, Museo Storia Nat, Florence, Italy Univ Fed Bahia, Salvador, BA, Brazil Fed Univ ABC, Sao Bernardo, Brazil Univ Fed Goias, Goiania, Go, Brazil Univ Alaska Museum, Fairbanks, AK USA Egerton Univ, Egerton, Kenya Museo Hist Nat, Lima, Peru IKIAM Univ Reg Amazon, Tena, Ecuador Univ Hyogo, Sanda, Japan Inst Rech Dev, Paris, France Univ Sao Paulo, Piracicaba, Brazil Niedersachs Landesbetrieb Wasserwirtschaft Kusten, Hannover, Germany Univ Complutense Madrid, Madrid, Spain Consejo Nacl Invest Cient & Tecn, Ctr Nacl Patagon, Puerto Madryn, Argentina Roosevelt Univ, Coll Profess Studies, Chicago, IL 60605 USA Western Kentucky Univ, Bowling Green, KY 42101 USA Univ Naples Federico II, Naples, Italy Univ Fed Acre, Rio Branco, Acre, Brazil Univ Fed Santa Catarina, Florianopolis, SC, Brazil Inst Bio & Geociencias Noroeste Argentino, Salta, Argentina Inst Venezolano Invest Cient, Caracas, Venezuela Umweltbundesamt, Vienna, Austria Penclen, Plumelec, France CNRS MNHN UPMC, Ctr Rech Paleobiodivers & Paleoenvironm, Paris, France Staatl Museum Nat Kunde, Stuttgart, Germany Consejo Nacl Invest Cient & Tecn, Museo Argentino Ciencias Nat Bernardino Rivada, Buenos Aires, DF, Argentina Ctr Biol Gest Populat INRA, Montferrier Sur Lez, France Loyola Univ Chicago, Chicago, IL USA Pontificia Univ Catolica Rio do Sul, Porto Alegre, RS, Brazil Durban Museum Nat Sci, Durban, South Africa Univ Estado Amazonas, Manaus, Amazonas, Brazil Brigham Young Univ, Provo, UT 84602 USA Museo Hist Nat La Salle, Caracas, Venezuela Univ Vet Med Hannover, Hannover, Germany Australian Museum, Sydney, NSW, Australia Texas Tech Univ, Lubbock, TX 79409 USA Francis Marion Univ, Florence, SC USA Univ Washington, Seattle, WA 98195 USA Univ Connecticut, Groton, CT USA Fed Univ ABC, Santo Andre, SP, Brazil Univ Fed Uberlandia, Uberlandia, MG, Brazil Fed Univ Para, Belem, Para, Brazil Yale Peabody Museum, New Haven, CT USA Univ Texas Arlington, Arlington, TX 76019 USA Senckenberg Deutsch Entomol Inst, Muncheberg, Germany CSIRO, Natl Res Collect, Canberra, ACT, Australia Univ Venda, Thohoyandou, South Africa Univ Ulsan, Ulsan, South Korea Univ Estadual Sao Paulo, Botucatu, SP, Brazil Senckenberg Forsch Inst & Nat Museum, Frankfurt, Germany Ocean Univ China, Inst Marine Biodivers & Evolut, Qingdao, Shandong, Peoples R China Univ Fed Para, Altamira, Brazil Univ Estadual Paulista, Assis, Brazil UPMC, Ctr Rech Paleobiodiversite & Paleoenvironm, CNRS, MNHN, Paris, France Tech Univ Kaiserslautern, Kaiserslautern, Germany Charles Univ Prague, Dept Zool, Prague, Czech Republic Univ Nacl Expt los Llanos Occident Ezequiel Zamor, Guanare, Venezuela Long Isl Univ, Brooklyn, NY USA Univ Ryukyus, Okinawa, Japan Pontificia Univ Catolica Ecuador, Museo Zool, Escuela Ciencias Biol, Quito, Ecuador Indiana Univ Penn, Indiana, PA USA IRD, Dakar, Senegal State Museum Nat Hist Karlsruhe, Karlsruhe, Germany Univ Toulouse III Paul Sabatier, Toulouse, France Univ Ghent, Ghent, Belgium Univ Antwerp, Antwerp, Belgium Karlsruhe Inst Technol, Karlsruhe, Germany Ctr Cellular & Mol Biol, Hyderabad, India Univ Fed ABC, Santo Andre, Brazil Yale Peabody Museum Nat Hist, New Haven, CT USA Univ Innsbruck, Mondsee, Austria Bethune Cookman Univ, Daytona Beach, FL USA Natl Museum Nat & Sci, Tokyo, Japan Zool Garten Koln, Cologne, Germany Univ Estadual Paulista, Botucatu, SP, Brazil Univ Estadual Paulista, Sao Vicente, Brazil Univ Estadual Paulista, Rio Claro, Brazil Univ Estadual Paulista, Sao Jose Do Rio Preto, Brazil Univ Estadual Paulista, Assis, Brazil

The ‘Mimic Octopus’Thaumoctopus mimicus Norman & Hochberg, 2005 exhibits a conspicuous primary defence mechanism (high-contrast colour pattern during ‘flatfish swimming’) that may involve facultative imperfect mimicry of conspicuous and/or inconspicuous models, both toxic and non-toxic (Soleidae and Bothidae). Here, we examine relationships between behavioural and morphological elements of conspicuous flatfish swimming in extant octopodids (Cephalopoda: Octopodidae), and reconstructed ancestral states, to examine potential influences on the evolution of this rare defence mechanism. We address the order of trait distribution to explore whether conspicuous flatfish swimming may be an exaptation that usurps a previously evolved form of locomotion for a new purpose. Contrary to our predictions, based on the relationships we examined, flatfish swimming appears to have evolved concurrently with extremely long arms, in a clade of sand-dwelling species. The conspicuous body colour pattern displayed by swimming T. mimicus may represent a secondary adaptation potentially allowing for mimicry of a toxic sole, improved disruptive coloration, and/or aposematic coloration. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 68–77.

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

Here we report the successful use of rolling circle amplification (RCA) for the amplification of complete metazoan mt genomes to make a product that is amenable to high-throughput genome sequencing techniques. The benefits of RCA over PCR are many and with further development and refinement of RCA, the sequencing of organellar genomics will require far less time and effort than current long PCR approaches.

The Gulf of California, Mexico, is often viewed as an insular environment for marine faunas. Moreover, its geographical history, geomorphology, latitudinal orientation and a convergence of three different water masses at the mouth of the Gulf make it an ideal setting for isolation, and probably contribute to the expectations of high endemism. However, rigorous analyses of biogeographic patterns are an essential prerequisite to an understanding of evolutionary processes in the Gulf and other biogeographic realms. A new 'sliding window' technique is presented here to test whether the Gulf of California is an isolated habitat. Endemism in the Gulf of California is evaluated by comparing the number of endemic gastropods for the Gulf of California with the number of endemic gastropods found in neighbouring coastlines of the same coastal length by using 'sliding window' analysis. Range sizes and diversity within the Gulf are compared with regions outside of the Gulf using variations of'sliding window' analysis. In addition, examining range endpoints and the percentage of ranges that lie across the mouth of the Gulf of California tests the hypothesis that the mouth acts as a barrier to migration into and out of the Gulf. The results of these analyses do not support the hypothesis that the nearshore Gulf of California faunas are structured by this supposed isolated body of water.

Ten new turtle taxa were described from pet trade specimens from China since the 1980s (see Fritz and Obst, 1998; Fritz and Obst, 1999; Parham et al., 2001 for a review). Specimens similar to one of these taxa, Cuora serrata Iverson and McCord, 1992 (originally Cuora galbinifrons serrata, elevated by Fritz and Obst, 1997), were shown to be hybrids of male Cuora mouhotii (Gray, 1862; formerly Pyxidea, but see Stuart and Parham, 2004) and females of Cuora galbinifrons Bourret, 1939 or Cuora bourreti Obst and Reimann, 1994 (Parham et al., 2001; and Stuart and Parham, 2004).

En este estudio se entrega un sistema de clasificación que refleja las relaciones de parentesco, inferidas a partir del análisis de la región 16S de ADN mitocondrial, de los patelogastrópodos que habitan en la zona intermareal a lo largo de la costa rocosa de Chile y Perú. Además, se incluye el análisis comparativo de estos patelogastrópodos en relación con la estructura, la morfología y los patrones de color de la concha, los dientes de la rádula y la anatomía corporal. Adicionalmente, se entrega información respecto de la distribución y ecología para todos los miembros de este grupo. Los resultados muestran que la fauna Lottiidae de Chile y Perú consiste en al menos nueve especies de patelogastrópodos intermareales. Esto es, ocho especies de patelogastrópodos agrupadas dentro del clado monofilético Scurria (S. variabilis, S. zebrina, S. viridula, S. plana, S. scurra, S. araucana, S. ceciliana y una especie no determinada) y un "taxón problemático" asignado preliminarmente dentro del género Lottia (Lottia orbignyi). El grupo está presente entre los 5º S y 54º S, registrándose en los niveles intermareales superior, medio e inferior, desde zonas expuestas a protegidas del oleaje. A nivel intraespecífico, los resultados nos permiten proponer la sinonimia de S. parasitica con S. variabilis, y de S. ceciliana con S. boehmita. Según esto, S. variabilis presentaría al menos tres ecofenotipos: (1) en sustratos rocosos a lo largo de todo su rango geográfico, (2) sobre las conchas de Fissurella crassa y F. limbata principalmente en Chile centro-sur y (3) sobre las placas del chitón Enoplochiton niger en el norte de Chile y sur del Perú. Por su parte, S. ceciliana es una especie de patelogastrópodo que presenta un patrón morfológico y de coloración de la concha altamente variable. En general, la alta variabilidad del patrón de color y morfología de la concha sitúa a estos patelogastrópodos entre los más complejos y diversos del mundo. Más aún, esta variabilidad y flexibilidad pueden ser responsables de las confusiones taxonómicas que han rodeado a este conjunto faunísticoIn this study we present a classification system reflecting the phylogenetic relationships for the intertidal patellogastropods of Chile and Peru. We infer phylogenetic relationships between limpets species using DNA sequences from the 16S region of the mitochondrial genome. We include a comparative limpet study of: shell structure, color and morphological patterns of the shell, radular teeth and anatomy. Additionally, we provide information about the distribution and ecology for members of this group within the studied area. The results show a Chilean-Peruvian Lottiidae fauna consisting of at least nine species, which are grouped into a single monophyletic clade Scurria (S. variabilis, S. zebrina, S. viridula, S. plana, S. scurra, S. araucana, S. ceciliana and a non identificated species), and a "problematic taxon" preliminarily assigned to the genus Lottia (Lottia orbignyi). The group of species is present in the intertidal rocky shores between 5º S and 54º S, from the upper to the lower intertidal fringes, ranging from exposed to protected areas. The systematic outcome of this study suggests the synonymization of S. parasitica to S. variabilis, and of S. ceciliana to S. boehmita. According to our field results, the species S. variabilis shows at least three ecophenotypes: (1) on rocky substrates along the full geographic range, (2) on the shells of the key-hole limpets: Fissurella crassa and F. limbata mainly in central and south of Chile, and (3) on the chiton plates of Enoplochiton niger in the north of Chile and south of Perú. S. ceciliana is a species in which morphology and color patterns are highly variable. In general, this variability indicates that the Chilean-Peruvian limpet species are among the most complex and diverse limpet fauna in the world. This, may reflects the taxonomic confusion which has beset this fauna

Rapa Nui is one of the most remote islands in the world. As a young island, its biota is a consequence of both natural dispersals over the last ~1 million years and recent human introductions. It therefore provides an opportunity to study a unique community assemblage. Here, we extract DNA from museum-preserved and newly field-collected spiders from the genus Tetragnatha to explore their history on Rapa Nui. Using an optimized protocol to recover ancient DNA from museum-preserved spiders, we sequence and assemble partial mitochondrial genomes from nine Tetragnatha species, two of which were found on Rapa Nui, and estimate the evolutionary relationships between these and other Tetragnatha species. Our phylogeny shows that the two Rapa Nui species are not closely related. One, the possibly extinct, T. paschae, is nested within a circumtropical species complex (T. nitens), and the other (Tetragnatha sp. Rapa Nui) appears to be a recent human introduction. Our results highlight the power of ancient DNA approaches in identifying cryptic and rare species, which can contribute to our understanding of the global distribution of biodiversity in all taxonomic lineages.

Recent studies investigating vicariance and dispersal have been focused on correlating major geological events with instances of taxonomic expansion by incorporating the fossil record with molecular clock analyses. However, this approach becomes problematic for soft-bodied organisms that are poorly represented in the fossil record. Here, we estimate the phylogenetic relationships of the nudibranch genus Acanthodoris Gray, 1850 using three molecular markers (16S, COI, H3), and then test two alternative geologically calibrated molecular clock scenarios in BEAST and their effect on ancestral area reconstruction (AAR) estimates employed in LAGRANGE. The global temperate distribution of Acanthodoris spans multiple geological barriers, including the Bering Strait (∼5.32 Mya) and the Baja Peninsula (∼5.5 Mya), both of which are used in our dating estimates. The expansion of the Atlantic Ocean (∼95-105 Mya) is also used to calibrate the relationship between A. falklandica Eliot, 1905 and A. planca Fahey and Valdes, 2005, which are distributed in southern Chile and South Africa respectively. Phylogenetic analyses recovered strong biogeographical signal and recovered two major clades representing northern and southern hemispheric distributions of Acanthodoris. When all three geological events are applied to the calibration analyses, the age for Acanthodoris is estimated to be mid-Cretaceous. When the expansion of the Atlantic Ocean is excluded from our analyses, however, Acanthodoris is estimated to be much younger, with a divergence time estimate during the Miocene. Regardless of divergence estimates, our AAR suggests that Acanthodoris may have origins in the Atlantic Ocean with the Atlantic acting as a dispersal point to the northeastern Pacific. These results suggest that Acanthodoris exhibits a rare instance of western trans-arctic expansion. This study also shows that northeast Pacific specimens of A. pilosa should be regarded as A. atrogriseata and that A. serpentinotus should be regarded as a synonym of A. pina.

Over the past 16 years, 13 new species of geoemydid turtles have been described from China. Ten of these new species are based on specimens purchased through the Hong Kong animal trade. Unfortunately, attempts by scientists to discover wild populations of some these newly described species have failed, raising questions about the legitimacy of the type localities and concerns over the validity of the species. Here the phylogenetic and taxonomic validity of two of these species is tested. Mitochondrial DNA haplotypes and allozyme genotypes of specimens matching the descriptions of Mauremys iversoni and Cuora serrata are compared to specimens of established species collected from known localities. The available evidence is consistent with the hypothesis that the specimens represent polyphyletic, intergeneric hybrids. The systematic status of all the new forms of turtles described from pet trade specimens are critical data for conservation efforts, particularly captive breeding.

Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced.

In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusksmore » and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.« less

Fourteen microsatellite markers were isolated and characterized from a microsatellite enriched genomic library obtained for the invasive red-eared slider turtle Trachemys scripta elegans (TSE). All but one locus conformed to Hardy–Weinberg equilibrium and none displayed linkage disequilibrium. The number of alleles ranged from 5 to 17 with observed heterozygosity values ranging from 0.26 to 0.96 for 23 individuals collected from its native range in the Mississippi River drainage. These markers will be useful in characterizing TSE populations and invaded populations of other Trachemys and could aid in the development of conservation management policies for invasive TSE.

En este estudio se entrega un sistema de clasificacion que refleja las relaciones de parentesco, inferidas a partir del analisis de la region 16S de ADN mitocondrial, de los patelogastropodos que habitan en la zona intermareal a lo largo de la costa rocosa de Chile y Peru. Ademas, se incluye el analisis comparativo de estos patelogastropodos en relacion con la estructura, la morfologia y los patrones de color de la concha, los dientes de la radula y la anatomia corporal. Adicionalmente, se entrega informacion respecto de la distribucion y ecologia para todos los miembros de este grupo. Los resultados muestran que la fauna Lottiidae de Chile y Peru consiste en al menos nueve especies de patelogastropodos intermareales. Esto es, ocho especies de patelogastropodos agrupadas dentro del clado monofiletico Scurria (S. variabilis, S. zebrina, S. viridula, S. plana, S. scurra, S. araucana, S. ceciliana y una especie no determinada) y un "taxon problematico" asignado preliminarmente dentro del genero Lottia (Lottia orbignyi). El grupo esta presente entre los 5o S y 54o S, registrandose en los niveles intermareales superior, medio e inferior, desde zonas expuestas a protegidas del oleaje. A nivel intraespecifico, los resultados nos permiten proponer la sinonimia de S. parasitica con S. variabilis, y de S. ceciliana con S. boehmita. Segun esto, S. variabilis presentaria al menos tres ecofenotipos: (1) en sustratos rocosos a lo largo de todo su rango geografico, (2) sobre las conchas de Fissurella crassa y F. limbata principalmente en Chile centro-sur y (3) sobre las placas del chiton Enoplochiton niger en el norte de Chile y sur del Peru. Por su parte, S. ceciliana es una especie de patelogastropodo que presenta un patron morfologico y de coloracion de la concha altamente variable. En general, la alta variabilidad del patron de color y morfologia de la concha situa a estos patelogastropodos entre los mas complejos y diversos del mundo. Mas aun, esta variabilidad y flexibilidad pueden ser responsables de las confusiones taxonomicas que han rodeado a este conjunto faunistico

Some errors occurred within Table 3 for which the publishers would like to apologise to their readers and the authors. The corrected Table 3 is below