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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.

Diverse mammal genomes open a new portal to hidden aspects of evolutionary history

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.

Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption of one-to-one relationships between names and biological entities breaks down (Remsen 2016, Franz and Sterner 2018). Taxonomic treatments and checklists provide authoritative information about the correct usage of names for species, including operational representations of the meanings of those names in the form of range maps, reference genetic sequences, or diagnostic traits. They increasingly provide taxonomic intelligence in the form of precise description of the semantic relationships between different published names in the literature. Making this authoritative information Findable, Accessible, Interoperable, and Reusable (FAIR; Wilkinson et al. 2016) would be a transformative advance for biodiversity data sharing and help drive adoption and novel extensions of existing standards such as the Taxonomic Concept Schema and the OpenBiodiv Ontology (Kennedy et al. 2006, Senderov et al. 2018). We call for the greater, global Biodiversity Information Standards (TDWG) and taxonomy community to commit to extending and expanding on how FAIR applies to biodiversity data and include practical targets and criteria for the publication and digitization of taxonomic concept representations and alignments in taxonomic treatments, checklists, and backbones. As a motivating case, consider the abundantly sampled North American deer mouse—Peromyscus maniculatus (Wagner 1845)—which was recently split from one continental species into five more narrowly defined forms, so that the name P. maniculatus is now only applied east of the Mississippi River (Bradley et al. 2019, Greenbaum et al. 2019). That single change instantly rendered ambiguous ~7% of North American mammal records in the Global Biodiversity Information Facility (n=242,663, downloaded 2021-06-04; GBIF.org 2021) and ⅓ of all National Ecological Observatory Network (NEON) small mammal samples (n=10,256, downloaded 2021-06-27). While this type of ambiguity is common in name-based databases when species are split, the example of P. maniculatus is particularly striking for its impact upon biological questions ranging from hantavirus surveillance in North America to studies of climate change impacts upon rodent life-history traits. Of special relevance to NEON sampling is recent evidence suggesting deer mice potentially transmit SARS-CoV-2 (Griffin et al. 2021). Automating the updating of occurrence records in such cases and others will require operational representations of taxonomic concepts—e.g., range maps, reference sequences, and diagnostic traits—that are FAIR in addition to taxonomic concept alignment information (Franz and Peet 2009). Despite steady progress, it remains difficult to find, access, and reuse authoritative information about how to apply taxonomic names even when it is already digitized. It can also be difficult to tell without manual inspection whether similar types of concept representations derived from multiple sources, such as range maps or reference sequences selected from different research articles or checklists, are in fact interoperable for a particular application. The issue is therefore different from important ongoing efforts to digitize trait information in species circumscriptions, for example, and focuses on how already digitized knowledge can best be packaged to inform human experts and artifical intelligence applications (Sterner and Franz 2017). We therefore propose developing community guidelines and criteria for FAIR taxonomic concept representations as "semantic artefacts" of general relevance to linked open data and life sciences research (Le Franc et al. 2020).

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.

Domestic and captive animals and cultivated plants should be recognised as integral components in contemporary ecosystems. They interact with wild organisms through such mechanisms as hybridization, predation, herbivory, competition and disease transmission and, in many cases, define ecosystem properties. Nevertheless, it is widespread practice for data on domestic, captive and cultivated organisms to be excluded from biodiversity repositories, such as natural history collections. Furthermore, there is a lack of integration of data collected about biodiversity in disciplines, such as agriculture, veterinary science, epidemiology and invasion science. Discipline-specific data are often intentionally excluded from integrative databases in order to maintain the “purity” of data on natural processes. Rather than being beneficial, we argue that this practise of data exclusivity greatly limits the utility of discipline-specific data for applications ranging from agricultural pest management to invasion biology, infectious disease prevention and community ecology. This problem can be resolved by data providers using standards to indicate whether the observed organism is of wild or domestic origin and by integrating their data with other biodiversity data (e.g. in the Global Biodiversity Information Facility). Doing so will enable efforts to integrate the full panorama of biodiversity knowledge across related disciplines to tackle pressing societal questions.

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.

Reconstructing how biodiversity arose is a fundamental goal of evolutionary biologists. Yet whether the fossil record or time-calibrated phylogenies of living species yield comparable evolutionary rate estimates is controversial, and possibly affected by the temporal scale of question being asked. Here we investigate diversification timing across mammals by comparing rate signatures in a credible set of molecular timetrees (N =5,911 species, ~ 70% from DNA) to those in fossil genus durations (N =5,262). Fossil-corrected and timetree-based rate estimates begin converging ~23 million years ago (Ma) and are equal at the present, in accord with progressively fewer unsampled extinctions ‘pulling’ on the timetree rates toward the present to cause underestimates. ‘Pushing’ the pulled timetree rates by means of fossil-recorded extinctions identifies a major pulse of speciation ~60 Ma, soon after the Cretaceous-Paleogene mass extinction event, due to the radiation of fossil stem lineages. For groups without substantial fossil records, all is not lost, however. We show that species-specific ‘tip’ rates of speciation are unbiased estimators of recent evolutionary processes; in turn, the clade-level skewness of tip rates approximates the extent of past shifts in net diversification. Molecular timetrees need fossil-correction to address deep-time questions, but timetrees are sufficient for shallower time questions for which extinctions are fewer and ecological diversity can be fully sampled.

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

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources have been developed to assemble trait data at the species level, but the underlying data and metadata about those trait measurements are often not reported, limiting broadest utility. Here we introduce FuTRES (Functional Trait Resource for Environmental Studies), a datastore and community resource for individual-level trait reporting that utilizes a strong semantic framework and best practices approach to overcome previous limitations. FuTRES already stores millions of trait measurements that span across multiple time scales, including zooarchaeological and paleobiological specimens, with a current focus on mammals. Two case studies showcase the promise of FuTRES. The first compares dynamically derived extant mammal species' body size estimates with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. The second shows that FuTRES data improves 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.

Mammals are unique in provisioning their offspring with milk, lactiferous nourishment produced in glandular organs called mammae. Mammae number is hypothesized to coevolve with litter size, acting as a constraint on offspring survival. However, predicted canonical relations between mammae number and litter size (i.e., the ‘one-half’ and ‘identity’ rules) are untested across Mammalia. Here we analyze data for 2,301 species and show how these characters coevolve. In Mammalia, mammae number approximates the maximum reported litter size of a species, and mammae number explains more variation in litter size than other species-level traits (mass, gestation length, diet, and seasonality of contemporary geographic distribution). Clades show differences in these patterns, indicating that certain life history strategies might break the ‘rules’ of mammary evolution. Mammae number is an underappreciated constraint on fecundity that has influenced the radiation of mammals.

A deep irony of COVID-19 likely originating from a bat-borne coronavirus (Boni et al. 2020) is that the global lockdown to quell the pandemic also locked up physical access to much basic knowledge regarding bat biology. Digital access to data on the ecology, geography, and taxonomy of potential viral reservoirs, from Southeast Asian horseshoe bats and pangolins to North American deer mice, was suddenly critical for understanding the disease's emergence and spread. However, much of this information lay inside rare books and personal files rather than as open, linked, and queryable resources on the internet. Even the world's experts on mammal taxonomy and zoonotic disease could not retrieve their data from shuttered laboratories. We were caught unprepared. Why, in this digitally connected age, were such fundamental data describing life on Earth not already freely accessible online? Understanding why biodiversity science was unprepared—and how to fix it before the next pandemic—has been the focus of our COVID-19 Taskforce since April 2020 and is continuing (organized by CETAF and DiSSCo). We are a group of museum-based and academic scientists with the goal of opening the rich ecological data stored in natural history collections to the research public. This information is rooted in what may seem an unlikely location—taxonomic names and their historical usages, which are the keys for searching literature and extracting linked ecological data (Fig. 1). This has been the core motivation of our group, enabled by the pioneering efforts of Plazi (Agosti and Egloff 2009) to build tools for literature digitization, extraction, and parsing (e.g., Synospecies, Ocellus) without which biodiversity science would be even less prepared. Our group led efforts to build an additional pipeline from Plazi to the Biodiversity Literature Repository at Zenodo, a free and unlimited data repository (Agosti et al. 2019), and then to GloBI, an open-source database of biotic interactions (Poelen et al. 2014, GloBI 2020). We also developed a direct integration from Pensoft Journals to GloBI, leveraging that publisher’s indexing of computer-readable terms (called semantic metadata; Senderov et al. 2018) to extract mammal host and virus information. Overall, considerable progress was made. In total, 85,492 new interactions were added to GloBI from 14 April to 21 May 2020 (see entire dataset on Zenodo: Poelen et al. 2020). Of those, 28,839 interactions are present when subset to "hasHost", "hostOf", "pathogenOf", "virus", and 4,101 unique name combinations are present after considering mammal species synonymies (from Meyer et al. 2015). Of those interactions, 892 species of mammals and 1,530 unique virus names are involved, which compares to 754 mammals and 586 viruses in the most recent data synthesis (Olival et al. 2017). While these liberated data may still include redundancies, they demonstrate the value of our approach and the expanse of known but digitally unconnected data that remains locked in publications. We can liberate host-virus data from publications, but doing so is expensive and does not scale to the continued influx of new articles that are inadequately digitized. Our efforts make it clear that Pensoft-style semantic publishing should be expanded to all major journals. The pandemic has created an opportunity for re-thinking the way we do science in the digital age. Thankfully, our future is not the past, so we do not have to keep wasting resources to digitially 'rediscover' biodiversity knowledge. We collectively call for changes to the publishing paradigm, so that research findings are directly accessible, citable, discoverable, and reusable for creating complete forms of digital knowledge.

We present a visual and interactive taxonomic Artificial Intelligence (AI) tool, the Automated Taxonomic Concept Reasoner (ATCR), whose graphical web interface is under development and will also become available via an Application Programming Interface (API). The tool employs automated reasoning (Beeson 2014) to align multiple taxonomies visually, in a web browser, using user or expert-provided taxonomic articulations, i.e. "Region Connection Calculus (RCC-5) relationships between taxonomic concepts, provided in a specific logical language (Fig. 1). It does this by representing the problem of taxonomic alignment under these constraints in terms of logical inference, while performing these inferences computationally and leveraging the powerful Microsoft Z3 Satisfiability Modulo Theory (SMT) solver (de Moura and Bjørner 2008). This tool represents further development of utilities for the taxonomic concept approach, which fundamentally addresses the challenge of robust biodiversity data aggregation in light of multiple conflicting sources (and source classifications) from which primary biodiversity data almost invariably originate. The approach has proven superior to aggregation, based just on the syntax and semantics provided by the Darwin Core standard Franz and Sterner 2018). Fig. 1 provides an artificial example of such an alignment. Two taxonomies, A and B, are shown. There are five taxonomic concepts, A.One, A.Two, A.Three, B.One and B.Two. A.Two and A.Three are sub-concepts (children) of A.One, and B.Two is a sub-concept (child) of B.One. These are represented by the direction of the grey arrows. The undirected mustard-coloured lines represent relationships, i.e., the articulations referred to in the previous paragraph. These may be of five kinds: congruent (==), includes (), overlap (> "sibling" concepts are disjoint in their instances, all instances of a parent concept are instances of at least one of its child concepts, and every concept has at least one instance - the SMT-based automated reasoner is able to deduce the relationships represented by the undirected green lines. It is also able to deduce disjunctive relationships where these are logically implied. "sibling" concepts are disjoint in their instances, all instances of a parent concept are instances of at least one of its child concepts, and every concept has at least one instance - the SMT-based automated reasoner is able to deduce the relationships represented by the undirected green lines. It is also able to deduce disjunctive relationships where these are logically implied. ATCR is related to Euler/X (Franz et al. 2015), an existing tool for the same kinds of taxonomic alignment problems, which was used, for example, to obtain an alignment of two influential primate classifications (Franz et al. 2016). It differs from Euler/X in that it employs a different logical encoding that enables more efficient and more informative computational reasoning, and also in that it provides a graphical web interface, which Euler/X does not.

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.

ispartof: Bioscience vol:70 issue:7 pages:531-534 status: published

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.

The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large- and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.

The insular radiation of hutias is remarkable among mammals for its high rate of extinction during the Holocene (∼58% of species), yet fragments of intact habitat throughout the West Indies retain a critical portion of endemic diversity needing assessment. Cuba contains 8 of the 11 recognized living species of hutias, with surviving forms also on Hispaniola, Jamaica, and the Bahamas. Herein, we performed molecular phylogenetic analyses across populations of Cuban hutias in the genera Capromys, Mesocapromys, and Mysateles to address major gaps in our understanding of their species limits, phylogenetic structure, and geographic distributions. Comparing sequences of mitochondrial genes (cyt-b, COI, 12S rRNA) from 41 individuals and 21 sites across the archipelago, we found evidence that Capromys pilorides contains a major species-level subdivision from western to eastern Cuba, spanning a greater geographic region than previously hypothesized. Populations of Capromys in each clade last shared a common ancestor ∼1.1 million years ago (Ma; 5.2% cyt-b divergence). The western clade is further subdivided between mainland hutias (C. p. pilorides) and those on Isla de la Juventud plus Cayo Cantiles (C. p. relictus has priority). The eastern clade contains all Capromys east of Sierra del Escambray in central Cuba, including mainland and insular forms. However, without paired analyses of morphology and genetics or data from type localities, we cannot assign a name to the eastern Capromys sp. nov. at this time. Divergencetime analyses across 9 named species of hutias (plus 1 extinct), including nuclear genes (GHR, vWF, RAG1), dates the Capromyidae split from their South American relatives (Echimyidae) at 15.5 Ma. The crown radiation of hutias was 8.8 Ma, with successive divergences at 5.4 Ma (Geocapromys), 3.1 Ma (Capromys), and 2.2 Ma (Mysateles–Mesocapromys). Detailed surveys are needed to assess the conservation status of these evolutionarily distinct Cuban taxa.

The majority (90%) of native terrestrial mammal species living in the Dominican Republic are bats, and two-thirds of these species are endemic to the Caribbean. However, recent molecular studies using DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 gene have suggested at least a 25% underestimation of biodiversity in bats throughout the world. A recent survey of bats in the Dominican Republic documented 15 of the 18 known species on the island of Hispaniola. Phylogenetic analysis of 132 individuals resulted in well-supported monophyletic species-level clades (maximal bootstrap values) with intraspecific variation ranging from 0% to 4.7% and interspecific variation ranging from 14.1% to 32.5%. A phylogeographic pattern separating the northern and southern Dominican Republic was recovered in 3 species of bats (Macrotus waterhousii, Pteronotus parnellii, and Pteronotus quadridens). The inclusion of broader geographic sampling across the Neotropics indicated that 3 widely distributed species (Eptesicus fuscus, Molossus molossus, and Monophyllus redmani) have high sequence divergence among insular or between insular and continental populations. Further systematic study is needed to identify morphologically cryptic species and their implications for conservation priorities in the Caribbean.

“What is crucial for your ability to communicate with me… pivots on the recipient’s capacity to interpret—to make good inferential sense of the meanings that the declarer is able to send” (Rescher 2000, p148). Conventional approaches to reconciling taxonomic information in biodiversity databases have been based on string matching for unique taxonomic name combinations (Kindt 2020, Norman et al. 2020). However, in their original context, these names pertain to specific usages or taxonomic concepts, which can subsequently vary for the same name as applied by different authors. Name-based synonym matching is a helpful first step (Guala 2016, Correia et al. 2018), but may still leave considerable ambiguity regarding proper usage (Fig. 1). Therefore, developing "taxonomic intelligence" is the bioinformatic challenge to adequately represent, and subsequently propagate, this complex name/usage interaction across trusted biodiversity data networks. How do we ensure that senders and recipients of biodiversity data not only can share messages but do so with “good inferential sense” of their respective meanings? Key obstacles have involved dealing with the complexity of taxonomic name/usage modifications through time, both in terms of accounting for and digitally representing the long histories of taxonomic change in most lineages. An important critique of proposals to use name-to-usage relationships for data aggregation has been the difficulty of scaling them up to reach comprehensive coverage, in contrast to name-based global taxonomic hierarchies (Bisby 2011). The Linnaean system of nomenclature has some unfortunate design limitations in this regard, in that taxonomic names are not unique identifiers, their meanings may change over time, and the names as a string of characters do not encode their proper usage, i.e., the name “Genus species” does not specify a source defining how to use the name correctly (Remsen 2016, Sterner and Franz 2017). In practice, many people provide taxonomic names in their datasets or publications but not a source specifying a usage. The information needed to map the relationships between names and usages in taxonomic monographs or revisions is typically not presented it in a machine-readable format. New approaches are making progress on these obstacles. Theoretical advances in the representation of taxonomic intelligence have made it increasingly possible to implement efficient querying and reasoning methods on name-usage relationships (Chen et al. 2014, Chawuthai et al. 2016, Franz et al. 2015). Perhaps most importantly, growing efforts to produce name-usage mappings on a medium scale by data providers and taxonomic authorities suggest an all-or-nothing approach is not required. Multiple high-profile biodiversity databases have implemented internal tools for explicitly tracking conflicting or dynamic taxonomic classifications, including eBird using concept relationships from AviBase (Lepage et al. 2014); NatureServe in its Biotics database; iNaturalist using its taxon framework (Loarie 2020); and the UNITE database for fungi (Nilsson et al. 2019). Other ongoing projects incorporating taxonomic intelligence include the Flora of Alaska (Flora of Alaska 2020), the Mammal Diversity Database (Mammal Diversity Database 2020) and PollardBase for butterfly population monitoring (Campbell et al. 2020).

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.

Biodiversity is distributed unevenly from the poles to the equator, and among branches of the tree of life, yet how those enigmatic patterns are related is unclear. We investigated global speciation-rate variation across crown Mammalia using a novel time-scaled phylogeny (N=5,911 species, ~70% with DNA), finding that trait- and latitude-associated speciation has caused uneven species richness among groups. We identify 24 branch-specific shifts in net diversification rates linked to ecological traits. Using time-slices to define clades, we show that speciation rates are a stronger predictor of clade richness than age. Speciation is slower in tropical than extra-tropical lineages, but only at the level of clades not species tips, consistent with fossil evidence that the latitudinal diversity gradient may be a relatively young phenomenon in mammals. In contrast, species tip rates are fastest in mammals that are low dispersal or diurnal, consistent with models of ephemeral speciation and ecological opportunity, respectively. These findings juxtapose nested levels of diversification, suggesting a central role of species turnover gradients in generating uneven patterns of modern biodiversity.

Analyses of morphological and molecular data indicate the existence of an unrecognized and unnamed species of soft-haired mouse, genus Abrothrix. Here, we name and describe this new species, which inhabits the Valdivian ecoregion, from the north of Chiloé Island onto the mainland in the Chilean regions of Los Lagos and Los Ríos; it also occurs at a single locality in the Argentinean province of Neuquén. Long confused with A. sanborni, the new species presents a unique combination of characters that differentiate it in external, cranial, phallic, and dental terms from its congeners. Phylogenetic analysis, based on cytochrome-b gene sequences, indicates that the new species is sister to a clade formed by the austral species A. lanosa and A. sanborni and differs on average from them by 5.7% and 5.2%, respectively. Results based on the nuclear Fgb-I7 locus are less conclusive regarding the phylogenetic position of the new species but also show its distinction. We comment on the conservation significance of our findings, considering that forests of the Valdivian ecoregion are suffering substantial human disturbance through intensive logging. Análisis de datos morfológicos y moleculares indican la existencia de una especie nueva e innominada de ratones del género Abrothrix. En este trabajo nominamos y describimos esta nueva especie que habita la ecorregión Valdiviana, desde el norte de la Isla de Chiloé hasta áreas continentales adyacentes de las regiones chilenas de Los Lagos y Los Ríos; la especie también ha sido registrada en una localidad de la provincia argentina del Neuquén. Largamente confundida con A. sanborni, la nueva especie presenta una combinación única de caracteres, incluyendo: coloración dorsal negruzca marrón oscuro a marrón-oliva; coloración ventral marrón grisácea a grisácea; cráneo delicado, con la constricción interorbital en forma de reloj de arena y caja craneana redondeada; rostro angosto y largo; nasales y premaxilares proyectados más anteriormente que los incisivos; placa cigomática estrecha; paladar extendiéndose apenas más allá del plano definido por el margen posterior de los M3; molares mesodontes; en adultos M1 sin flexo anteromedio; parastilo y mesolofo presentes; estómago unilocular-hemiglandular; cráter terminal del pene dirigido ventralmente; elementos apicales cartilaginosos ausentes. Análisis filogenéticos basados en secuencias del gen del citocromo b indican que la nueva especie es hermana de un clado formado por las especies australes A. lanosa y A. sanborni y que difiere de éstas en promedio 5.7 % y 5.2 %, respectivamente. Resultados basados en el locus nuclear beta fibrinógeno son menos conclusivos en relación a la posición filogenética de la nueva especie, aunque también muestran su distinción. Considerando que la ecorregión Valdiviana está sufriendo un impacto antrópico substancial, finalizamos el trabajo comentando sobre la relevancia de nuestro hallazgo para la biología de la conservación. Fil: D Elía, Guillermo. Universidad Austral de Chile; Chile Fil: Teta, Pablo Vicente. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Upham, Nathan S.. Integrative Research Center; Estados Unidos. McMaster University; Canadá Fil: Pardiñas, Ulises Francisco J.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina Fil: Patterson, Bruce. Integrative Research Center; Estados Unidos

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

The Ctenohystrica is one of the three major lineages of rodents and contains diverse forms related to gundis, porcupines, and guinea pigs. Phylogenetic analyses of this group using mitochondrial and nuclear gene sequences confirm the monophyly of the infraorder Hystricognathi and most of its recognized subclades, including both the Neotropical caviomorphs and the African phiomorphs, which are recovered as sister groups. Molecular timetrees calibrated with 22 securely placed fossils indicate that hystricognath superfamilies originated in the Eocene and Oligocene and most families had appeared by the end of the Oligocene, ∼23 Mya. Divergences leading to hystricognath genera took place in the Miocene and Pliocene, with a single exception. The naked mole-rat (Heterocephalus) diverged from other African mole-rats (Bathyergidae) in the early Oligocene (∼31.2 Mya), when the four caviomorph superfamilies (Erethizonoidea and Cavioidea at 32.4 Mya, Chinchilloidea and Octodontoidea at 32.8 Mya) were first appearing in South America. The extended independent evolution of Heterocephalus suggested by this analysis prompted a closer examination of mole-rat characters. Heterocephalus indeed shares many characters with bathyergids, befitting their joint membership in the parvorder Bathyergomorphi and superfamily Bathyergoidea as well as their shared exploitation of subterranean lifestyles. However, a diverse array of cranial, dental, postcranial, external, and ecological characters distinguishes Heterocephalus from other African mole-rats. These differences equal or exceed those used to diagnose caviomorph families and justify recognizing the naked mole-rat in its own family, Heterocephalidae Landry, 1957. This taxonomic arrangement poses questions for the inter-relationships of fossil and extant mole-rats and brings time equivalence to the ranks assigned to the major clades of hystricognaths. © 2014 The Linnean Society of London

Rodents make foraging decisions by balancing demands to acquire energy and mates with the need to avoid predators. To identify variations in the risk of predation, nocturnal rodents may use moonlight as a cue of risk. Moonlight avoidance behaviors have been observed in many nocturnal rodent species and are widely generalized to small mammals. However, most prior studies have been limited to 1 species or 1 study site, or occurred in modified habitats. We evaluated desert rodent activity patterns in natural habitats from 1999 to 2006 at 62 study sites across the Great Basin Desert of western North America. Rodent activity was examined by livetrapping in open habitats, using the presence of the sand-obligate kangaroo mouse (Microdipodops) as a habitat indicator. Activity patterns were assessed on 69 nights with clear skies and compared to corresponding moonlight values (moon phase and brightness) to evaluate the frequency of moonlight avoidance. Analyses of total activity of all species in the rodent assemblage relative to moonlight showed a distinct nonrandom (triangular-shaped) pattern but no significant correlations. However, individual genera of desert rodents responded differently to moonlight. Only kangaroo rats (Dipodomys) displayed significant moonlight avoidance patterns; they were maximally active at significantly different moonlight levels and avoided bright moonlight to a greater extent than co-occurring rodents. Moonlight seemed to limit the activity of kangaroo rats most strongly on bright nights during waxing moon phases and summer seasons, but not significantly during the spring or fall seasons, or during waning moons. Rather than avoiding moonlight, the activity of deer mice (Peromyscus), pocket mice (Perognathus), and kangaroo mice may be governed by changes in competition with kangaroo rats. Differences in the body size, locomotion, and space use of kangaroo rats relative to other rodents may explain why different moonlight responses were detected, especially if these traits alter how rodents perceive risk from bright moonlight. These findings indicate that moonlight avoidance may be a specialized trait of kangaroo rats rather than a general behavior of nocturnal desert rodents in the Great Basin.

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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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, 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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

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.

The two currently recognized species of kangaroo mice, Microdipodops megacephalus and M. pallidus, inhabit sandy soils of the Great Basin Desert in western North America. Given their habitat specificity and the fluctuating climate throughout the Pleistocene, kangaroo mice likely endured a turbulent biogeographic history that resulted in disjunct distributions and isolation of genetic lineages. Recent phylogenetic investigations using mitochondrial data have revealed several mitochondrial clades within this genus that may represent cryptic species. These mitochondrial clades are genetically unique, occupy relatively small distributions, and, as such, may be at an increased risk of extinction due to climate change and extensive recent habitat alteration. Herein, we apply haplotype network, population genetic, and historical demographic analyses to mitochondrial data of each Micropdipodops species and mitochondrial clade to assess conservation genetics within kangaroo mice. Results indicate that each mitochondrial clade is a distinct lineage with little to no gene flow occurring among clades. Additionally, historical demographic analyses support past population expansions and identify locations of past refugium for each distinct lineage. Although mitochondrial data indicate that the clades appear to be in approximate genetic equilibrium and have not suffered any extreme bottlenecks over time, there is still concern for the survival of smaller and more vulnerable Microdipodops subpopulations due to impending habitat threats in the Great Basin Desert.

Aim The rodent genus Microdipodops (kangaroo mice) includes two sand-obligate endemics of the Great Basin Desert: M. megacephalus and M. pallidus. The dark kangaroo mouse, M. megacephalus, is distributed throughout the Great Basin and our principal aims were to formulate phylogenetic hypotheses for this taxon and make phylogeographical comparisons with its congener. Location The Great Basin Desert of western North America. Methods DNA sequence data from three mitochondrial genes were examined from 186 individuals of M. megacephalus, representing 47 general localities. Phylogenetic inference was used to analyse the sequence data. Directional analysis of phylogeographical patterns was used to examine haplotype sharing patterns and recover routes of gene exchange. Haplotype–area curves were constructed to evaluate the relationship between genetic variation and distributional island size for M. megacephalus and M. pallidus. Results Microdipodops megacephalus is a rare desert rodent (trapping success was 2.67%). Temporal comparison of trapping data shows that kangaroo mice are becoming less abundant in the study area. The distribution has changed slightly since the 1930s but many northern populations now appear to be small, fragmented, or locally extinct. Four principal phylogroups (the Idaho isolate and the western, central and eastern clades) are evident; mean sequence divergence between phylogroups for cytochrome b is c. 8%. Data from haplotype sharing show two trends: a north–south trend and a web-shaped trend. Analyses of haplotype–area curves reveal significant positive relationships. Main conclusions The four phylogroups of M. megacephalus appear to represent morphologically cryptic species; in comparison, a companion study revealed two cryptic lineages in M. pallidus. Estimated divergence times of the principal clades of M. megacephalus (c. 2–4 Ma) indicate that these kangaroo mice were Pleistocene invaders into the Great Basin coincident with the formation of sandy habitats. The north–south and web patterns from directional analyses reveal past routes of gene flow and provide evidence for source–sink population regulation. The web pattern was not seen in the companion study of M. pallidus. Significant haplotype–area curves indicate that the distributional islands are now in approximate genetic equilibrium. The patterns described here are potentially useful to conservation biologists and wildlife managers and may serve as a model for other sand-obligate organisms of the Great Basin.

Lessa et al. (2014) make a compelling casefor systematic exploration of genomes inthe diverse South American rodent fauna.Not only do the caviomorph and sigmod-ontine rodents comprise a sizable portionof the continental fauna, but they haveradiated into virtually all available habi-tats and have adopted practically all of thelife modes exploited by rodents elsewhere.Both are diverse and demonstrably mono-phyletic, offering great insights into theevolutionary transitions underlying thesepresumably adaptive radiations. Here wecomment on the non-South Americanportions of these radiations, as well asthe broader phylogenetic context of theserodents, recent work on Caribbean taxa,and historical biogeography.Although both rodent radiationsflourished in South America, neitheris confined there, as clearly noted by theauthors.BothgroupsextendfarintoNorthAmerica, reaching the Arctic Ocean inthe case of the caviomorph