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"Lee, Thomas E."
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Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches
Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers ( RBP3 , GHR , RAG1 , Cytb ) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys . Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi ) in the genus Neusticomys ( sensu stricto ), and the recognition of at least two new species (one in Neusticomys , one in Daptomys ). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.
Journal Article
A new species of Andean mouse of the genus Thomasomys (Cricetidae, Sigmodontinae) from the eastern Andes of Ecuador
We name and describe a new species of Andean mouse from the eastern slope of the Andes of central Ecuador (Sangay National Park). This rodent is large-bodied (head-body length 167–184 mm) inhabiting the wet montane forest between 3,400–3,900 m in elevation. A molecular phylogeny based on mitochondrial genes resolved the new species as a member of the “aureus” group, closely related to an undescribed species from north Ecuador. This finding increases the diversity of Thomasomys to 48 species, of which 18 species inhabit Ecuador. In addition, the species described herein is the largest species of the genus described in Ecuador.
Journal Article
Back to the future: A preserved specimen validates the presence of Molossus pretiosus (Molossidae, Chiroptera) in Honduras
Molossus pretiosus is a molossid bat that has been thought to exist in Honduras. While some authors have suggested its range extends all the way to Mexico, others have placed its northernmost distribution in Nicaragua. We present evidence, based on one specimen collected in 2005, confirming the presence of this species in the Caribbean of Honduras within the Islas de la Bahía department. This discovery increases the count of known species within this family to 18 in the country and raises the total bat species count for Honduras to 114. We recommend a detailed study of historical specimens to confirm the identification of species that may have been misidentified as well as a thorough examination of molossids distributed in northern Honduras.
Journal Article
Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
Journal Article
Global Diversity and Distribution of Hantaviruses and Their Hosts
Rodents represent 42% of the world’s mammalian biodiversity encompassing 2,277 species populating every continent (except Antarctica) and are reservoir hosts for a wide diversity of disease agents. Thus, knowing the identity, diversity, host–pathogen relationships, and geographic distribution of rodent-borne zoonotic pathogens, is essential for predicting and mitigating zoonotic disease outbreaks. Hantaviruses are hosted by numerous rodent reservoirs. However, the diversity of rodents harboring hantaviruses is likely unknown because research is biased toward specific reservoir hosts and viruses. An up-to-date, systematic review covering all known rodent hosts is lacking. Herein, we document gaps in our knowledge of the diversity and distribution of rodent species that host hantaviruses. Of the currently recognized 681 cricetid, 730 murid, 61 nesomyid, and 278 sciurid species, we determined that 11.3, 2.1, 1.6, and 1.1%, respectively, have known associations with hantaviruses. The diversity of hantaviruses hosted by rodents and their distribution among host species supports a reassessment of the paradigm that each virus is associated with a single-host species. We examine these host–virus associations on a global taxonomic and geographical scale with emphasis on the rodent host diversity and distribution. Previous reviews have been centered on the viruses and not the mammalian hosts. Thus, we provide a perspective not previously addressed.
Journal Article