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opencc-zeroFeb 2020View details →

Data from: Two new species of Serjania (Sapindaceae) from Michoacán, Mexico, with notes on S. biternata

Serjania rosalindae and S. crucensis (Sapindaceae-Paullinieae), new species from the municipality of La Huacana, Michoacán, Mexico, are described, illustrated, and compared with closely related species. In addition, micromorphological features of the leaves, flowers, and pollen grains are investigated. A treatment of the endemic S. biternata from Guerrero is also included because it is a little-known taxon similar to S. rosalindae whose fruits were previously unknown. All of these taxa share capsules that are chartaceous to almost woody and septifragal, a fruit type otherwise uncommon within Serjania. The distinctive fruit morphology of these species is discussed in relation to other species of Serjania.

Data from: New Cretaceous lungfishes (Dipnoi, Ceratodontidae) from western North America

Ceratodontid lungfishes are generally rare, poorly represented elements of North America's Mesozoic ecosystems, with previously known maximum diversity in the Late Jurassic. Herein we describe four new species of the form genus Ceratodus, from the Cretaceous of the Western Interior, considerably expanding fossil representation of post-Triassic dipnoans in North America. To model taxonomic and morphologic diversity, we adopt a four-fold system of phenetically based species groups, named for exemplars from the Morrison Formation. Ceratodus kirklandi n. sp. (Potamoceratodus guentheri group) and C. kempae n. sp. (C. frazieri group) represent a hitherto unsampled time interval, the Valanginian. Ceratodus nirumbee n. sp. and C. molossus n. sp. extend the temporal ranges of the C. fossanovum and C. robustus groups upward to the Albian and Cenomanian, respectively. These new occurrences show that ceratodontids maintained their highest diversity from the Late Jurassic through the mid-Cretaceous (Albian–Cenomanian), an interval of ~60 Myr. The existing record suggests that some of the later (mid-Cretaceous) ceratodontids may have been tolerant of salt water; to date, there is no evidence that they aestivated. Only a few occurrences are known from horizons younger than Cenomanian. Demise of ceratodontids appears to be part of a broader pattern of turnover that occurred at the Cenomanian-Turonian boundary in North America.

opencc-zeroDec 2017View details →

Data from: Geographic variation of body size in new world anurans: energy and water in a balance

The validity of Bergmann's rule, perhaps the best known ecogeographical rule, has been questioned for ectothermic species. Here, we explore the interspecific version of the rule documenting body size gradients for anurans across the whole New World and evaluating which environmental variables best explain the observed patterns. We assembled a dataset of body sizes for 2761 anuran species of the Western Hemisphere and conducted assemblage-based and cross-species analyses that consider the spatial and phylogenetic structure in the data. In accordance with heat and water-related explanations for body size clines, we found a consistent association of median body size and potential evapotranspiration across the New World. A relevant role of water availability also emerges, suggesting the joint importance of body size for thermoregulation and hydroregulation in anurans. Anurans do not follow a simple Bergmannian pattern of increasing size towards high latitudes. Consistent with previous regional findings, our Hemisphere-wide analyses detect that the geographic variation in anuran body sizes is highly dependent on a trade-off between heat and water balance. The observed size-climate relationships possibly emerge from the interplay between thermoregulatory abilities and the benefits inherent to reduced surface-to-volume ratios in larger species, which decrease the rates of evaporative water loss and favour heat retention. Our results also show how temperature becomes important for species that are directly in contact with the substrate and water, like burrowing and terrestrial anurans, while arboreal species exhibit a body size cline linked with potential evapotranspiration.

opencc-zeroDec 2013View details →

Data from: A new species of the paper wasp genus Polistes (Hymenoptera, Vespidae, Polistinae) in Europe revealed by morphometrics and molecular analyses

We combine multivariate ratio analysis (MRA) of body measurements and analyses of mitochondrial and nuclear data to examine the status of several species of European paper wasps (Polistes Latreille, 1802) closely related to P. gallicus. Our analyses unambiguously reveal the presence of a cryptic species in Europe, as two distinct species can be recognized in what has hitherto been considered Polistes bischoffi Weyrauch, 1937. One species is almost as light coloured as P. gallicus, and is mainly recorded from Southern Europe and Western Asia. The other species is darker and has a more northern distribution in Central Europe. Both species occur syntopically in Switzerland. Given that the lost lectotype of P. bischoffi originated from Sardinia, we selected a female of the southern species as a neotype. The northern species is described as P. helveticus sp. n. here. We also provide a redescription of P. bischoffi rev. stat. and an identification key including three more closely related species, P. biglumis, P. gallicus and P. hellenicus.

opencc-zeroDec 2017View details →

Data from: A new species of Pittosporum described from the Poor Knights Islands, Northland, Aotearoa/New Zealand

Here we describe Pittosporum roimata Gemmill & S.N. Carter, the only vascular plant endemic to the Poor Knights Islands, Northland, Aotearoa/New Zealand. This new species has previously been referred to as a distinct variant of Pittosporum cornifolium (tāwhiri karo, wharewhareatua), a morphologically similar epiphytic shrub known from both main islands of New Zealand as well as other off shore islands. We have segregated this new species from P. cornifolium based on morphology, DNA sequence variation, as well as distribution. Pittosporum roimata is distinguished from P. cornifolium by a number of characters, including having larger thicker leaves with shorter petioles, flowers with yellow petals, larger inflorescences, and producing several terminal fruits per stem. Pittosporum roimata is locally common on the islands of Tawhiti Rahi, Aorangi, and Aorangaia, growing on rocky substrates associated with Xeronema callistemon (raupo taranga) and Metrosideros excelsa (pōhutukawa). Using the current New Zealand Threat Classification System, we suggest a preliminary classification of this new species as 'At Risk / Naturally Uncommon' qualified DP [Data Poor), OL [One Location].

Data from: A systematic review of cetothere baleen whales (Cetacea, Cetotheriidae) from the Late Miocene of Crimea and Caucasus, with a new genus

Nine taxa of Miocene baleen whales were described from the Black Sea region under the name Cetotherium before 1951, and a further four closely related species representing three genera have been added in recent years. This rich diversity requires taxonomic revision and ordering. Here, a new genus, Mithridatocetus, is described from the Tortonian of Crimea and Caucasus, with two species, M. eichwaldi and M. adygeicus (originally Kurdalagonus adygeicus); 'Cetotherium' mayeri (a nomen dubium) is also a member of this genus. In comparison with other Cetotheriinae, Mithridatocetus is distinguished by the autapomorphic shape of the tympanic bulla with the swollen main ridge, the lowered anterior portion of the involucrum and the oblique anterolateral margin; such synapomorphies, as a transversely narrow squamosal with the ventromedially oriented postglenoid process (shared with Eucetotherium), a squamosal cleft (shared with Kurdalagonus) and an oval surface of the compound posterior process of the tympanoperiotic on the posterolateral skull wall (shared with Brandtocetus); and a unique combination of a high neurocranium and a long and robust paroccipital process. The genus Kurdalagonus is redefined here as containing only one described species, K. mchedlidzei. Therefore, the group Cetotheriinae is now restricted to the latest Serravallian and Tortonian of the Eastern Paratethys and includes at least five genera: Cetotherium, Brandtocetus, Kurdalagonus, Mithridatocetus and Zygiocetus. In addition, ?Cetotherium priscum and C. incertum are considered to be nomina dubia; 'Cetotherium' klinderi and 'Cetotherium' pusillum require more complete specimens for reassessment; 'Cetotherium' maicopicum and Eucetotherium helmersenii require further research to identify their taxonomical affinities.

Data from: Phylogeny and temporal diversification of the New World pond turtles (Emydidae)

We present a comprehensive multigene phylogeny and time tree for the turtle family Emydidae. Our phylogenetic analysis, based on 30 nuclear and four mitochondrial genes (23,330 total base pairs) sequenced for two individuals for each of the currently recognized species of the subfamily Emydinae and two species from each of the more species-rich Deirochelyinae genera, yielded a well-supported tree that provides an evolutionary framework for this well-studied clade and a basis for a stable taxonomy. We calibrated an emydid time tree using three well-vetted fossils, modeled uncertainty in fossil ages to reflect their accuracy in node dating, and extracted stem/crown ages of a number of key diversification events. We date the age of crown emydids at a relatively young 44 Ma, and the crown age of both contained subfamilies at roughly 30 Ma. One deirochelyine clade, which includes the genera Graptemys, Malaclemys, Pseudemys, and Trachemys and contains 11% of all turtle species, dates to 21 Ma just prior to the mid-Miocene climatic optimum, suggesting a potential causal link between warm, moist conditions and rapid species accumulation of these highly aquatic turtles. Both nuclear DNA data alone and in combination with mitochondrial DNA support the monophyly of an inclusive genus Emys containing the old world species orbicularis and trinacris and the new world blandingii, marmorata and pallida. Given that all members of this group were originally aligned in the genus Emys and that the age of the clade is roughly equal to other emydine genera, we strongly support a classification that places these five species in a single genus rather than the alternative three-genus scheme (Emys (orbicularis, trinacris), Actinemys (marmorata, pallida), Emydoidea (blandingii). The phylogeny and resulting time tree presented here provides a comprehensive foundation for future comparative analyses of the Emydidae that will shed light on the historical ecology and conservation prioritization of this diverse chelonian clade.

Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community-level data set. We collected 1,195 gastropods and crabs in British Columbia. First, the General mixed Yule-coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species-hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co-occurrence patterns for non-randomness using community-wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species-hypotheses in community-level datasets. Non-random species co-occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of opportunistic omnivorous gastropods and crabs appeared influenced by random processes. Species-pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co-occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.

Data from: Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood

Phragmotic or "door head" ants have evolved independently in several ant genera across the world, but in Africa only one case has been documented until now. Carebara elmenteitae (Patrizi) is known from only a single phragmotic major worker collected from sifted leaf-litter near Lake Elmenteita in Kenya, but here the worker castes of two species collected from Kakamega Forest, a small rainforest in Western Kenya, are studied. Phragmotic major workers were previously identified as Carebara elmenteitae and non-phragmotic major and minor workers were assigned to C. thoracica (Weber). Using evidence of both morphological and next-generation sequencing analysis, it is shown that phragmotic and non-phragmotic workers of the two different species are actually the same and that neither name – C. elmenteitae or C. thoracica – correctly applies to them. Instead, this and another closely related species from Ivory Coast are both morphologically different from C. elmenteitae, and thus they are described as the new species Carebara phragmotica sp. n. and Carebara lilith sp. n.

Data from: A new barcheek darter species from Buck Creek (Cumberland River System), Kentucky (Percidae: Etheostomatinae: Catonotus: Oopareia)

Etheostoma nebra, the Buck Darter, is described as a new species endemic to the Buck Creek system of the Cumberland River drainage in Kentucky, USA. The earliest collection records of Etheostoma nebra date to 1955 and were considered a population of Etheostoma virgatum. Etheostoma nebra is delimited through morphological comparisons with Etheostoma virgatum and phylogenetic analyses using DNA sequences from a mitochondrial gene and five nuclear genes. Etheostoma nebra is distinguished from Etheostoma virgatum by a lower number of total lateral scales, fewer pored lateral scales and modally 13 compared with 12 pectoral fin rays. The two species also differ in patterns of pigmentation and nuptial male coloration. In the molecular phylogenies, Etheostoma nebra is not resolved as the sister species of Etheostoma virgatum. A review of all museum collection records of Etheostoma nebra and extensive field surveys in the Buck Creek system demonstrate a dramatic decline of the species over the past 30 years. Collections made from 1955 to 1981 show that Etheostoma nebra was widespread throughout the Buck Creek system, but the species is currently restricted to a small portion of Flat Lick Creek. Etheostoma nebra is critically imperiled based on its restricted geographic distribution and documented disappearance of populations within the Buck Creek system during the past three decades.

Data from: A new monster from southwest Oregon forests: Cryptomaster behemoth sp. n. (Opiliones, Laniatores, Travunioidea)

The monotypic genus Cryptomaster Briggs, 1969 was described based on individuals from a single locality in southwestern Oregon. The described species C. leviathan Briggs, 1969 was named for its large body size compared to most travunioid Laniatores. However, as the generic name suggests, Cryptomaster are notoriously difficult to find, and few subsequent collections have been recorded for this genus. Here, we increase sampling of Cryptomaster to 15 localities, extending their known range from the Coast Range northeast to the western Cascade Mountains of southern Oregon. Phylogenetic analyses of mitochondrial and nuclear DNA sequence data reveal deep phylogenetic breaks consistent with independently evolving lineages. We use discovery and validation species delimitation approaches to generate and test species hypotheses, including a coalescent species delimitation method to test multi-species hypotheses. For delimited species, we use light microscopy and SEM to discover diagnostic morphological characters. Although Cryptomaster has a small geographic distribution, this taxon is consistent with other short-range endemics in having deep phylogenetic breaks indicative of species level divergences. Herein we describe Cryptomaster behemoth sp. n., and provide morphological diagnostic characters for identifying C. leviathan and C. behemoth.

opencc-zeroDec 2016View details →

Data from: New taxa and a case of ephemeral spore production in Lecideaceae from western North America

Cyclohymenia epilithica is a newly described genus and species from Oregon and Washington, U.S.A. It occurs on noncalcareous rock in the oceanic forests west of the crest of the Cascade Range. Unlike most other North American species in the Lecideaceae, it is restricted to shady habitats in cool, wet, temperate climates. It is distinguished from other members of the family by its thick, pale gray green, epilithic thallus; immersed apothecia that superficially appear like perithecia or pycnidia; and ascocarps that usually contain a central sterile column surrounded by a ring-shaped hymenium. The structure and position of the ascocarp appear to be unique among Lecideaceae and related families. The species is also unusual in producing short-lived asci; most collections have barren apothecia. Lecidea atrobrunnea subsp. deplanaica is raised to the species level. The taxon deserves specific rank, not just from its distinctive chemistry, but also from morphology, distribution, and ecology that differ from L. atrobrunnea s.str. The newly described Lecidea uniformis from Oregon and Washington, mainly west of the Cascade crest, is similar in many ways to L. fuscoatra, but the areoles are uniformly brown and do not have a differentiated gray, blackish, or whitish edge. DNA sequence data support the taxa Cyclohymenia epilithica and L. uniformis.

Data from: Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia.

Southeastern Asia is a recognised hotspot for emerging infectious diseases, many of which have an animal origin. Mammarenavirus infections contribute significantly to the human disease burden in both Africa and the Americas, but little data exists for Asia. To date only two mammarenaviruses, the widely spread lymphocytic choriomeningitis virus and the recently described Wēnzhōu virus have been identified in this region, but the zoonotic impact in Asia remains unknown. Here we report the presence of a novel mammarenavirus and of a genetic variant of the Wēnzhōu virus and provide evidence of mammarenavirus-associated human infection in Asia. The association of these viruses with widely distributed mammals of diverse species, commonly found in human dwellings and in peridomestic habitats, illustrates the potential for widespread zoonotic transmission and adds to the known aetiologies of infectious diseases for this region.

opencc-zeroDec 2012View details →

Data from: Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant Angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range-wide genetic diversity based on nuclear microsatellite data, and detected four well-differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modeled the ecological niche of Amborella based on current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of suitable habitat at the last glacial maximum (LGM, ca. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra- and inter-specific diversity in New Caledonian plants, and revealed the possibility of an as-yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographic history of an emblematic taxon.

Data from: Candelariella clarkii and Lecidea hoganii: two lichen species new to science from White Rocks Open Space, City of Boulder, Colorado

Two new species are described from vouchers collected as part of an intensive lichen inventory of Fox Hills Sandstone outcrops in an open space preserve within the city limits of Boulder, Colorado. Candelariella clarkii is characterized by its cryptolecanorine apothecia, chartreuse areolate thallus, and 8-spored asci. Lecidea hoganii is a member of the L. auriculata morphological group characterized by a thick white chalky thallus, pink pigments in the hymenium, and absence of secondary compounds. We provide IUCN conservation assessments for both new species, which should be considered critically endangered. The discovery of two species new to science in a relatively densely populated region of North America illustrates the ecological relevance of small of patches of native habitat, which are certain to become even more important in the future.

Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each situated on islands on either side of Wallace's Line. One radiation is composed of Philippine species of Platymantis and the other contains all taxa from the eastern Indonesian, New Guinean, Solomon, Bismarck, and Fijian archipelagos. Several additional genera (Batrachylodes, Discodeles, Ceratobatrachus, and Palmatorappia) are nested within Platymantis, and of these Batrachylodes and Discodeles are nonmonophyletic. To address the widespread paraphyly of the genus Platymantis and several additional nomenclatural issues, we undertook a wholesale nomenclatural reorganization of the family. Given our partially unresolved phylogeny, and in order to impart a conservative, stable taxonomy, involving a minimal number of genus-species couplet changes, we propose a conservative classification representing a few compromises. These changes are designed to preserve maximally the presumed original intent of taxonomy (widely used group names associated with morphological and ecological diversity of particular species or groups of species) while implementing a hierarchical system that is consistent with the estimate of phylogeny based on new molecular data.

opencc-zeroJun 2019View details →

Data from: Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): new genomic tools for breeding programs and management of natural resources

The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non-native species and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980's and showed some degree of innate resistance (long-term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis, and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.

Data from: The cat-eyed snakes of Madagascar: phylogeny and description of a new species of Madagascarophis (Serpentes: Lamprophiidae) from the tsingy of Ankarana

The cat-eyed snakes of the genus Madagascarophis are among the most commonly encountered snake species in Madagascar. Yet despite their broad distribution and frequent occurrence in human-disturbed habitat, Madagascarophis still contains unrecognized species diversity. Here, we describe a new species of Malagasy cat-eyed snake from a specimen found in the tsingy karst system of Ankarana in northern Madagascar. Using multiple loci from all currently described species, including the never-before-sequenced M. ocellatus, we delimit a new species and also determine its placement within the genus in a Bayesian coalescent framework, using BPP and *BEAST, respectively. Our results indicate that molecular data are sufficient to delimit this new taxon. These data also support its placement as the sister taxon to the recently described M. fuchsi which is endemic to the Montagne des Français karst massif also in northern Madagascar. We also provide a morphological description of this new snake species, which can be readily diagnosed based on external morphological characters, and include a species identification key for the entire genus based on external morphology.

opencc-zeroDec 2012View details →

Data from: Population biology of establishment in New Zealand hedgehogs inferred from genetic and historical data: conflict or compromise?

The crucial steps in biological invasions, related to the shaping of genetic architecture and the current evolution of adaptations to a novel environment, usually occur in small populations during the phases of introduction and establishment. However, these processes are difficult to track in nature due to invasion lag, large geographic and temporal scales compared with human observation capabilities, the frequent depletion of genetic variance, admixture and other phenomena. In this study, we compared genetic and historical evidence related to the invasion of the West European hedgehog to New Zealand to infer details about the introduction and establishment. Historical information indicates that the species was initially established on the South Island. A molecular assay of populations from Great Britain and New Zealand using mitochondrial sequences and nuclear microsatellite loci was performed based on a set of analyses including approximate Bayesian computation, a powerful approach for disentangling complex population demographies. According to these analyses, the population of the North Island was most similar to that of the native area and showed greatest reduction in genetic variation caused by founder demography and/or drift. This evidence indicated the location of the establishment phase. The hypothesis was corroborated by data on climate and urbanization. We discuss the contrasting results obtained by the molecular and historical approaches in the light of their different explanatory power and the possible biases influencing the description of particular aspects of invasions, and we advocate the integration of the two types of approaches in invasion biology.