37 Works

Data from: High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

Santiago Sanchez-Ramirez, Rampal S. Etienne & Jean-Marc Moncalvo
Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity build-up, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well-recognized pattern describing a decline in species richness from the equator pole-wards. Recent macroecological studies in ectomycorrhizal (EM) fungi have shown that their LDG is shifted, peaking at temperate rather than tropical...

Data from: Testing for ancient adaptive radiations in Neotropical cichlid fishes

Hernán López-Fernández, Jessica H. Arbour, Kirk O. Winemiller & Rodney L. Honeycutt
Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether patterns of lineage and morphological diversification are congruent with hypothesized adaptive radiations in South and Central America. We found that diversification in the Neotropical cichlid clade and...

Data from: Shaping species with ephemeral boundaries: the distribution and genetic structure of the desert tortoise (Gopherus morafkai) in the Sonoran Desert region

Taylor Edwards, Mercy Vaughn, Philip C. Rosen, Cristina Meléndez Torres, Alice E. Karl, Melanie Culver & Robert W. Murphy
Aim: We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity. Location: Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA. Methods: We examined wild...

Data from: Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage

Roger B. J. Benson, Nicolás E. Campione, Matthew T. Carrano, Philip D. Mannion, Corwin Sullivan, Paul Upchurch & David C. Evans
Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation,...

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)

Yunhe Wu, Fang Yan, Bryan L. Stuart, Elizabeth Prendini, Chatmongkon Suwannapoom, Hollis A. Dahn, Bao-Lin Zhang, Hong-Xia Cai, Yong-Biao Xu, Ke Jiang, Hong-Man Chen, Alan R. Lemmon, Emily Moriarty Lemmon, Christopher J. Raxworthy, Nikolai L. Orlov, Robert W. Murphy & Jing Che
Amolops is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus...

Interrogating discordance resolves relationships in the rapid radiation of Old World fruit bats (Chiroptera: Pteropodidae)

Nicolas Nesi, Stephen Rossiter, Michael McGowen, Georgia Tsagkogeorga, Burton Lim, Susan Tsang, Violaine Nicolas, Aude Lalis, Silke Riesle Sbarbaro, Sigit Wiantoro, Alan Hitch, Javier Juste, Corinna Pinzari, Frank Bonaccorso, Nancy Simmons, Annette Scanlon & Christopher Todd
The family Pteropodidae (Old World fruit bats) comprises >200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with >50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the...

Data from: The Collins’ monster, a spinous suspension-feeding lobopodian from the Cambrian Burgess Shale of British Columbia

Jean-Bernard Caron & Cédric Aria
Lobopodians, a paraphyletic group of Palaeozoic vermiform animals bearing metameric appendages, are key to the origin of extant panarthropods. First discovered in 1983 on Mount Stephen (Yoho National Park, British Columbia), the Cambrian (Wuliuan) Burgess Shale lobopodian nicknamed “Collins’ monster” is formally described as Collinsovermis monstruosus gen. et sp. nov. A formal systematic revision of the poorly known lobopodian Acinocricus stichus from Utah is also provided. The body of Collinsovermis is plump and compact, lacking...

Data from: In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex

Santiago Sánchez-Ramirez, Rodham E. Tulloss, Laura Guzmán-Davalos, Joaquín Cifuentes-Blanco, Ricardo Valenzuela, Arturo Estrada-Torres, Felipe Ruán-Soto, Raúl Díaz-Moreno, Nallely Hernández-Rico, Mariano Torres-Gómez, Hugo León & Jean-Marc Moncalvo
Some of the effects of past climate dynamics on plant and animal diversity make-up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbor high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion is expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve...

Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics

Scott V. Edwards, Alison Cloutier & Allan J. Baker
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the...

Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

Katriina L. Ilves & Hernán López-Fernández
Cichlid fishes (family Cichlidae) are models for evolutionary and ecological research. Massively parallel sequencing approaches have been successfully applied to study relatively recent diversification in groups of African and Neotropical cichlids, but such technologies have yet to be used for addressing larger scale phylogenetic questions of cichlid evolution. Here we describe a process for identifying putative single-copy exons from five African cichlid genomes and sequence the targeted exons for a range of divergent (> tens...

Data from: Testing of the effect of missing data estimation and distribution in morphometric multivariate data analyses

Caleb Marshall Brown, Jessica H. Arbour & Donald A. Jackson
Missing data are an unavoidable problem in biological datasets and the performance of missing data deletion and estimation techniques in morphometric datasets are poorly understood. Here a novel method is used to measure the introduced error of multiple techniques on a representative sample. A large sample of extant crocodilian skulls was measured and analyzed with principal components analysis (PCA). Twenty-three different proportions of missing data were introduced into the dataset, estimated, analyzed, and compared to...

Exceptional multifunctionality in the feeding apparatus of a mid-Cambrian radiodont

Joseph Moysiuk & Jean-Bernard Caron
Radiodonts (stem Euarthropoda) were ecologically diverse, but species generally displayed limited functional specialization of appendages along the body axis compared to crown group euarthropods. This is puzzling because such functional specialization is considered to have been an important driver of euarthropod ecological diversification. One way to circumvent this constraint could have been the functional specialization of different parts of the frontal appendages, known to have been ecologically important in radiodonts. This hypothesis has yet to...

Data from: Systematics of spiny-backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

Karl-Heinz Jungfer, Julián Faivovich, José M. Padial, Santiago Castroviejo-Fisher, Mariana M. Lyra, Bianca Von Muller Berneck, Patricia P. Iglesias, Philippe J. R. Kok, Ross T. Macculloch, Miguel Trefaut Rodrigues, Vanessa K. Verdade, Claudia P. Torres Gastello, Juan Carlos Chaparro, Paula H. Valdujo, Steffen Reichle, Jiří Moravec, Václav Gvoždík, Giussepe Gagliardi-Urrutia, Raffael Ernst, Ignacio De La Riva, Donald Bruce Means, Albertina P. Lima, J. Celsa Señaris, Ward C. Wheeler & Célio F. B. Haddad
Spiny-backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly...

Data from: New Middle Cambrian bivalved arthropod from the Burgess Shale (British Columbia, Canada)

David A. Legg & Jean-Bernard Caron
The morphology of two new bivalved arthropods, Loricicaris spinocaudatus gen. et sp. nov. and Nereocaris briggsi sp. nov. from the middle Cambrian (Series 3, Stage 5) Burgess Shale Formation (Collins Quarry locality on Mount Stephen, Yoho National Park, British Columbia, Canada), is described. The material was originally assigned to the genus Branchiocaris, but exhibits distinctive character combinations meriting its assignment to other taxa. Loricicaris spinocaudatus possesses an elongate and spinose abdomen comparable to the contemporaneous...

Relatedness and the composition of communities over time: evaluating phylogenetic community structure in the late Cenozoic record of bivalves

Lucy Chang & Phillip Skipwith
Understanding the mechanisms that prevent or promote the coexistence of taxa at local scales is critical to understanding how biodiversity is maintained. Competitive exclusion and environmental filtering are two processes thought to limit which taxa become established in a community. However, determining the relative importance of the two processes is a complex task, especially when the critical initial stages of colonization cannot be directly observed. Here, we explore the use of phylogenetic community structure for...

Morphology and osteohistology of a large-bodied caenagnathid (Theropoda: Oviraptorosauria) from the Hell Creek Formation (Montana): implications for size-based classifications and growth reconstruction in theropods

Thomas Cullen, D. Jade Simon, Elizabeth Benner & David Evans
Oviraptorosaurs, like many coelurosaurians, are frequently diagnosed using incomplete or fragmentary skeletal remains, with factors such as body size often used to assign material to a particular taxon or as a basis for describing new species. Here we describe a partial skeleton, ROM VP 65884, from the Hell Creek Formation (Montana), and through morphological and phylogenetic comparisons identify it as belonging to Caenagnathidae, and likely referable to Anzu wyliei. We perform multi-element osteohistological sampling of...

Data from: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Hao-Chih Kuo, Shiang-Fan Chen, Yin-Ping Fang, James A. Cotton, Joe D. Parker, Gábor Csorba, Burton K. Lim, Judith L. Eger, Chia-Hong Chen, Cheng-Han Chou & Stephen J. Rossiter
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between...

Data from: The fragmentation of Pangaea and Mesozoic terrestrial vertebrate biodiversity

Matthew J. Vavrek
During the Mesozoic (242–66 million years ago), terrestrial regions underwent a massive shift in their size, position and connectivity. At the beginning of the era, the land masses were joined into a single supercontinent called Pangaea. However, by the end of the Mesozoic, terrestrial regions had become highly fragmented, both owing to the drifting apart of the continental plates and the extremely high sea levels that flooded and divided many regions. How terrestrial biodiversity was...

Data from: A large new leanchoiliid from the Burgess Shale and the influence of inapplicable states on stem arthropod phylogeny

Cédric Aria, Jean-Bernard Caron & Robert Gaines
Characterized by atypical frontalmost appendages, leanchoiliids are early arthropods whose phylogenetic placement has been much debated. Morphological interpretations have differed, some of which concern critical characters such as the number of eyes and head appendages, but methodological approaches also have diverged. Here, we describe a new leanchoiliid, Yawunik kootenayi gen. et sp. nov., based on 42 specimens from the newly discovered Marble Canyon locality of the Burgess Shale (Kootenay National Park, British Columbia; middle Cambrian)....

Data from: How do seasonality, substrate, and management history influence macrofungal fruiting assemblages in a central Amazonian Forest?

Dirce Leimi Komura, Jean-Marc Moncalvo, Cristian S. Dambros, Larissa S. Bento, Maria A. Neves & Charles E. Zartman
Worldwide, fungal richness peaks in tropical forest biomes where they are the primary drivers of decomposition. Understanding how environmental and anthropogenic factors influence tropical macrofungal fruiting patterns should provide insight as to how, for example, climate change and deforestation may impact their long-term demographic stability and evolutionary potential. However, in Amazonia no studies have yet to disentangle the effects of substrate, seasonality and forest history on phenology. Here, we quantitate spatial and temporal variation in...

Data from: Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes)

Jessica H. Arbour & Hernan López-Fernández
Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity...

Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Taylor Edwards, Marc Tollis, PingHsun Hsieh, Ryan N. Gutenkunst, Zhen Liu, Kenro Kusumi, Melanie Culver & Robert W. Murphy
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus....

Data from: A new family of Cambrian rhynchonelliformean brachiopods (Order Naukatida) with an aberrant coral-like morphology

Michael Streng, Aodhán D. Butler, John S. Peel, Russell J. Garwood & Jean-Bernard Caron
Tomteluva perturbata gen. et sp. nov. and Nasakia thulensis gen. et sp. nov., two new rhynchonelliformean brachiopod taxa, are described from carbonate beds from the lower middle Cambrian (Series 3, Stage 5) basinal Stephen Formation, Canada, and the upper lower Cambrian (Series 2, Stage 4) Henson Gletscher Formation, North Greenland, respectively. The two taxa are characterized by an unusual coral-like morphology typified by a high conical ventral valve with an anteriorly curved umbo and a...

Data from: A new species of Peckoltia from the Upper Orinoco (Siluriformes: Loricariidae)

Jonathan Armbruster, Nathan Lujan, Jonathan W. Armbruster & Nathan K. Lujan
A new species of the suckermouth armored catfish genus Peckoltia is described from the lower Ventuari River, a tributary of the upper Orinoco River in Amazonas State, Venezuela. Specimens of this species were formerly included in the wide-ranging Amazonian species P. vittata, but a recent molecular phylogeny found Orinoco individuals to be distantly related to Amazon Basin individuals spanning the range of P. vittata syntypes. Detailed morphological examination confirmed distinctiveness of Orinoco specimens, and found...

Data from: Three new naraoiid species from the Burgess Shale, with a morphometric and phylogenetic reinvestigation of Naraoiidae

Benjamin Mayers, Cédric Aria & Jean-Bernard Caron
Naraoiids are non‐biomineralized euarthropods characterized by the complete fusion of post‐cephalic tergo‐pleurae into a single shield, as well as an extensively ramified digestive tract. Ranging from the early Cambrian to the late Silurian (Pridoli), these arthropods of simple appearance have traditionally been associated with the early diversification of trilobites and their close relatives, but the interrelationships and affinities of naraoiids within Artiopoda remain poorly characterized. Three new species from the Burgess Shale (middle Cambrian, Stage...

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