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The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns – but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans., Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.

Bats harbour a diverse array of viruses, some of which are zoonotic, and are one of the most speciose groups of mammals on earth. As part of an ongoing bat-associated viral diversity research project, we identified three cycloviruses (family Circoviridae) in fecal samples of silver-haired bats (Lasionycteris noctivagans) caught in Cave Creek Canyon of Arizona (USA). Two of the three identified genomes represent two new species in the genus Cyclovirus. Cycloviruses have been found in a wide range of environments and hosts; however, little is known about their biology. These new genomes of cycloviruses are the first from silver-haired bats, adding to the broader knowledge of cyclovirus diversity. With continuing studies, it is likely that additional viruses of the family Circoviridae will be identified in Arizona bat populations.

Ungulate migrations are crucial for maintaining abundant populations and functional ecosystems. However, little is known about how or why migratory behaviour evolved in ungulates. To investigate the evolutionary origins of ungulate migration, we employed phylogenetic path analysis using a comprehensive species-level phylogeny of mammals. We found that 95 of 207 extant ungulate species are at least partially migratory, with migratory behaviour originating independently in 17 lineages. The evolution of migratory behaviour is associated with reliance on grass forage and living at higher latitudes wherein seasonal resource waves are most prevalent. Indeed, originations coincide with mid-Miocene cooling and the subsequent rise of C

To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled an ecological trait data set for 18,016 species of terrestrial vertebrates and utilized phylogenetic comparative methods to test which categories of habitat association, mode of locomotion, and feeding mode best predicted extinction risk. We also examined the individual categories of the International Union for Conservation of Nature Red List extinction drivers (e.g., agriculture and logging) threatening each species and determined the greatest threats for each of the four terrestrial vertebrate groups. We then quantified the sum of extinction drivers threatening each species to provide a multistressor perspective on threat. Cave dwelling amphibians (p0.01), arboreal quadrupedal mammals (all of which are primates) (p0.01), aerial and scavenging birds (p0.01), and pedal (i.e., walking) squamates (p0.01) were all disproportionately threatened with extinction in comparison with the other assessed ecological traits. Across all threatened vertebrate species in the study, the most common risk factors were agriculture, threatening 4491 species, followed by logging, threatening 3187 species, and then invasive species and disease, threatening 2053 species. Species at higher risk of extinction were simultaneously at risk from a greater number of threat types. If left unabated, the disproportionate loss of species with certain functional traits and increasing anthropogenic pressures are likely to disrupt ecosystem functions globally. A shift in focus from species- to trait-centric conservation practices will allow for protection of at-risk functional diversity from regional to global scales.Una Señal Ecológica Mundial del Riesgo de Extinción de los Vertebrados Terrestres Resumen Construimos un conjunto de datos de atributos ecológicos de 18,016 especies de vertebrados terrestres y utilizamos métodos de comparación filogenética para analizar cuáles categorías de asociación de hábitat, modo de locomoción y modo de alimentación predicen de mejor manera el riesgo de extinción. Lo anterior lo hicimos para determinar la distribución y las causas de las amenazas de extinción a lo largo de los grupos funcionales de vertebrados terrestres. También examinamos las categorías individuales de los factores de extinción (p. ej.: agricultura, tala de árboles) de la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza que amenazan a cada especie y determinamos las principales amenazas para cada uno de los cuatro grupos de vertebrados terrestres. Después cuantificamos la suma de los factores de extinción que amenazan a cada especie para proporcionar una perspectiva de estresores múltiples sobre la amenaza. Los anfibios cavernícolas (p0.01), mamíferos arbóreos cuadrúpedos (todos son primates) (p0.01), aves aéreas y carroñeras (p0.01) y los escamados caminantes (p0.01) tuvieron una amenaza de extinción desproporcionada en comparación con los otros atributos ecológicos analizados. En todas las especies de vertebrados que estudiamos, los factores de riesgo más comunes fueron la agricultura, que amenaza a 4,491 especies, y la deforestación, que amenaza a 3,187 especies; le siguen las especies invasoras y las enfermedades, que juntas amenazan a 2,053 especies. Las especies con el mayor riesgo de extinción también se encontraban simultáneamente en riesgo por un mayor número de tipos de amenazas. Si esto se mantiene constante, la pérdida desproporcionada de especies con ciertos atributos funcionales y la creciente presión antropogénica probablemente alteren las funciones ecosistémicas a nivel mundial. Un cambio en el enfoque de las prácticas de conservación, de estar centradas en la especie a estar centradas en los atributos, permitirá la protección de la diversidad funcional en riesgo desde la escala regional hasta la global.

Preventing extinctions requires understanding macroecological patterns of vulnerability or persistence. However, correlates of risk can be nonlinear, within-species risk varies geographically, and current-day threats cannot reveal drivers of past losses. We investigated factors that regulated survival or extinction in Caribbean mammals, which have experienced the globally highest level of human-caused postglacial mammalian extinctions, and included all extinct and extant Holocene island populations of non-volant species (219 survivals or extinctions across 118 islands). Extinction selectivity shows a statistically detectable and complex body mass effect, with survival probability decreasing for both mass extremes, indicating that intermediate-sized species have been more resilient. A strong interaction between mass and age of first human arrival provides quantitative evidence of larger mammals going extinct on the earliest islands colonized, revealing an extinction filter caused by past human activities. Survival probability increases on islands with lower mean elevation (mostly small cays acting as offshore refugia) and decreases with more frequent hurricanes, highlighting the risk of extreme weather events and rising sea levels to surviving species on low-lying cays. These findings demonstrate the interplay between intrinsic biology, regional ecology and specific local threats, providing insights for understanding drivers of biodiversity loss across island systems and fragmented habitats worldwide.

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pronounced few-tress), an online datastore and community resource for individual-level trait reporting that utilizes a semantic framework. FuTRES already stores millions of trait measurements for paleobiological, zooarchaeological, and modern specimens, with a current focus on mammals. We compare dynamically derived extant mammal species' body size measurements in FuTRES with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. We then show that individual-level data improve estimates of body mass-including uncertainty-for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.

Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems. ispartof: LANCET PLANETARY HEALTH vol:5 issue:10 pages:E746-E750 ispartof: location:Netherlands status: published

What should the best practices be for modeling zoonotic disease risks, e.g. to anticipate the next pandemic, when background assumptions are unsettled or evolving rapidly? This challenge runs deeper than one might expect, all the way into how we model the robustness of contemporary phylogenetic inference and taxonomic classifications. Different and legitimate taxonomic assumptions can destabilize the putative objectivity of zoonotic risk assessments, thus potentially supporting inconsistent and overconfident policy decisions.

Summary Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to "pull" speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or "push" the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66–56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific "tip" rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade's extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our “backbone-and-patch” approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level “patch” phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded (“DNA-only” trees) or imputed within taxonomic constraints using branch lengths drawn from local birth–death models (“completed” trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous “supertree” approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology., This study presents a newly robust evolutionary timescale for ~6000 extant species of mammals, aimed at understanding their species-specific rates of diversification and distinct phylogenetic history. Ages and relationships in the tree of life are estimated with probabilistic confidence levels to help future tests of eco-evolutionary hypotheses.

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about five million years ago. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrarae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared to the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects ? including during the evolution of hypersaline dietary tolerance in T. barrerae. Fil: Evans, Ben J.. Mc Master University; Canadá Fil: Upham, Nathan S.. Mc Master University; Canadá. Field Museum of Natural History; Estados Unidos. University of Yale; Estados Unidos Fil: Golding, G. Brian. Mc Master University; Canadá Fil: Ojeda, Ricardo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina Fil: Ojeda, Agustina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina

International audience; Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.

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No. of bitstreams: 0 Previous issue date: 2016-11-23 Villanova Univ, Dept Biol, Villanova, PA 19085 USA Museu Nacl Hist Nat & Ciencia, Lisbon, Portugal Univ Brasilia, Dept Zool, Inst Ciencias Biol, BR-70910900 Brasilia, DF, Brazil Smithsonian Inst, Natl Museum Nat Hist, Washington, DC 20560 USA Sorbonne Univ, Museum Natl Hist Nat, ISYEB, Paris, France Univ Nacl Tucuman, San Miguel De Tucuman, Argentina King Saud Univ, Riyadh, Saudi Arabia Cornell Univ, Ithaca, NY USA Univ Fed Sao Paulo, Diadema, Brazil Upper Austrian Museum, Ctr Biol, Linz, Austria Villanova Univ, Villanova, PA 19085 USA Univ Salzburg, Salzburg, Austria Plazi, Bern, Switzerland Univ Brasilia, Brasilia, DF, Brazil Univ Sao Paulo, Ribeirao Preto, Brazil Zool Forsch Museum A Koenig, Bonn, Germany Museu Paraense Emilio Goeldi, Belem, Para, Brazil Russian Acad Sci, St Petersburg, Russia Pontificia Univ Catolica Rio Grande do Sul, Porto Alegre, RS, Brazil Museo Reg Sci Nat, Turin, Italy Univ Fed Rio Grande do Sul, Porto 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, Bengaluru, India Univ Nebraska, Lincoln, NE USA CENAK Ctr Nat Kunde, Hamburg, Germany Ohio Hist Connect, Columbus, OH USA Univ Fed Amazonas, Manaus, Amazonas, Brazil Univ Malaga, Malaga, Spain Chinese Acad Sci, Qingdao, Shandong, Peoples R China Benemerita Univ Autonoma Puebla, Puebla, Mexico Natl Polytech Inst, Ctr Res & Adv Studies, Irapuato, Mexico Field Museum Nat Hist, Chicago, IL 60605 USA Univ Texas El Paso, El Paso, TX 79968 USA Univ Fed Lavras, Lavras, Brazil Nat Hist Museum, Vienna, Austria La Sierra Univ, Riverside, CA USA Univ San Francisco Quito, Quito, Ecuador Univ Hong Kong, Hong Kong, Peoples R China CUNY, New York, NY 10021 USA CAS, Inst Vertebrate Biol, Brno, Czech Republic Sorbonne Univ, MECADEV, Museum Natl Hist Nat, Paris, France Univ Estadual Paulista, Rio Claro, Brazil Zool Staatssammlung Munchen, Munich, Germany Univ Michigan, Dearborn, MI 48128 USA Smithsonian Inst, Natl Museum Nat Hist, Washington, DC USA Helmholtz Ctr Environm Res, Leipzig, Germany Santa Rosa 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

Evolutionary radiations on continents are less well-understood and appreciated than those occurring on islands. The extent of ecological influence on species divergence can be evaluated to determine whether a radiation was ultimately the outcome of divergent natural selection or else arose mainly by nonecological divergence. Here, we used phylogenetic comparative methods to test distinct hypotheses corresponding to adaptive and nonadaptive evolutionary scenarios for the morphological evolution of sigmodontine rodents. Results showed that ecological variables (diet and life-mode) explain little of the shape and size variation of sigmodontine skulls and mandibles. A Brownian model with varying rates for insectivory versus all other diets was the most likely evolutionary model. The insectivorous sigmodontines have a faster rate of morphological evolution than mice feeding on other diets, possibly due to stronger selection for features that aid insectivory. We also demonstrate that rapid early-lineage diversification is not accompanied by high morphological divergence among subclades, contrasting with island results. The geographic size of continents permits spatial segregation to a greater extent than on islands, allowing for allopatric distributions and escape from interspecific competition. We suggest that continental radiations of rodents are likely to produce a pattern of high species diversification coupled with a low degree of phenotypic specialization.

Background The tropical Andes and Amazon are among the richest regions of endemism for mammals, and each has given rise to extensive in situ radiations. Various animal lineages have radiated ex situ after colonizing one of these regions from the other: Amazonian clades of dendrobatid frogs and passerine birds may have Andean ancestry, and transitions from the Amazon to Andes may be even more common. To examine biogeographic transitions between these regions, we investigated the evolutionary history of three clades of rodents in the family Echimyidae: bamboo rats (Dactylomys-Olallamys-Kannabateomys), spiny tree-rats (Mesomys-Lonchothrix), and brush-tailed rats (Isothrix). Each clade is distributed in both the Andes and Amazonia, and is more diverse in the lowlands. We used two mitochondrial (cyt- b and 12S) and three nuclear (GHR, vWF, and RAG1) markers to reconstruct their phylogenetic relationships. Tree topologies and ancestral geographic ranges were then used to determine whether Andean forms were basal to or derived from lowland radiations. Results Four biogeographic transitions are identified among the generic radiations. The bamboo rat clade unambiguously originated in the Amazon ca. 9 Ma, followed by either one early transition to the Andes (Olallamys) and a later move to the Amazon (Dactylomys), or two later shifts to the Andes (one in each genus). The Andean species of both Dactylomys and Isothrix are sister to their lowland species, raising the possibility that highland forms colonized the Amazon Basin. However, uncertainty in their reconstructed ancestral ranges obscures the origin of these transitions. The lone Andean species of Mesomys is confidently nested within the lowland radiation, thereby indicating an Amazon-to-Andes transition ca. 2 Ma. Conclusions Differences in the timing of these biogeographic transitions do not appear to explain the different polarities of these trees. Instead, even within the radiation of a single family, both Andean and Amazonian centers of endemism appear enriched by lineages that originated in the other region. Our survey of other South American lineages suggests a pattern of reciprocal exchange between these regions—among mammals, birds, amphibians, and insects we found no fewer than 87 transitions between the Andes and Amazon from Miocene-Pleistocene. Because no clear trend emerges between the timing and polarity of transitions, or in their relative frequency, we suggest that reciprocal exchange between tropical highland and lowland faunas in South America has been a continual process since ca. 12 Ma.

The rodent superfamily Octodontoidea comprises 6 families, 38 genera, and 193 living species of spiny rats, tuco-tucos, degus, hutias, and their relatives. All are endemic to the Neotropical Region where they represent roughly three-quarters of extant caviomorphs. Although caviomorph monophyly is well established and phylogenetic hypotheses exist for several families, understanding of octodontoid relationships is clouded by sparse taxon sampling and single-gene analyses. We examined sequence variation in one mitochondrial (12S rRNA) and three nuclear genes (vWF, GHR, and RAG1) across all caviomorph families (including 47 octodontoid species), all phiomorph families, and the sole remaining hystricognath family, using the gundi ( Ctenodactylus ) and springhaas ( Pedetes ) as outgroups. Our analyses support the monophyly of Phiomorpha, Caviomorpha, and the caviomorph superfamilies Cavioidea (Dasyproctidae, Cuniculidae, and Caviidae, the latter including Hydrochoerus ), Erethizontoidea, Chinchilloidea (including Dinomyidae), and Octodontoidea. Cavioids and erethizontoids are strongly supported as sisters, whereas chinchilloids appear to be sister to octodontoids. Among octodontoids, Abrocomidae is consistently recovered as the basal element, sister to a pair of strongly supported clades; one includes Octodontidae and Ctenomyidae as reciprocally monophyletic lineages, whereas the other includes taxa currently allocated to Echimyidae, Capromyidae and Myocastoridae. Capromys appears near the base of this clade, in keeping with current classification, but Myocastor is nested securely inside a clade of Echimyidae that also contains eumysopines, echimyines and dactylomyines. Another, more weakly supported clade of Echimyidae contains fossorial and scansorial taxa from the Chaco–Cerrado–Caatinga and the Atlantic Forest. Biogeographic analyses robustly recover the Patagonia–Southern Andes complex as ancestral for the Octodontoidea, with three component lineages emerging by the Oligocene–Miocene boundary (∼23 Ma): (1) stem abrocomids in the Central and Southern Andes; (2) a lineage leading to octodontids plus ctenomyids in Patagonia, later dispersing into the Chaco–Cerrado–Caatinga; and (3) a lineage leading to echimyids, capromyids, and myocastorids that subsequently radiated in more mesic biomes, including Amazonia, Atlantic Forest, and the Antilles. This reconstruction refutes earlier ideas that the diverse, generalized, mainly lowland family Echimyidae, which appears early in the fossil record, gave rise to the Andean lineages of octodontoids—instead, the reverse derivation appears to be true. We recommend formal synonymy of Myocastoridae with Echimyidae but defer a similar treatment of Capromyidae until additional hutia taxa and sequences can be analyzed.