phylogeny

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. …

Disease detection in historical samples currently relies on DNA extraction and amplification, or immunoassays. These techniques only …

How ecological opportunity relates to diversification is a central question in evolutionary biology. However, there are few empirical …

Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the …

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous song- birds endemic to South America. We delimited species based on examination of >600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsi- mony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underesti- mated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recov- ered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.

Aim To test the hypothesis that Caribbean Short‐faced bats descended from a single recent ancestor that originated in the continental Neotropics (Mexico, Central America and/or South America). Location The Neotropics, including the West Indies. Methods New mitochondrial cytochrome b and nuclear Rag2 sequences were combined with published molecular data to estimate phylogenetic relationships and sequence divergence among Short‐faced bats. The resulting phylogenies were compared with those compatible with the single‐origin hypothesis using two model‐based statistical tests. Confidence limits on sequence divergence were estimated using a parametric bootstrap. Results All molecular phylogenies revealed two independent Caribbean lineages and showed that continental Short‐faced bats share a recent common ancestor. Morphology‐based trees compatible with the single‐origin hypothesis were significantly worse at explaining the molecular data than any molecular phylogeny. Main conclusions The ancestor of all Short‐faced bats reached the Antilles in the Miocene, too recently to have used a proposed Oligocene land bridge, and well before the Pleistocene glaciations that are thought to have facilitated dispersal for many bats. After a long period of isolation, Short‐faced bats diversified quickly on the Caribbean islands. A single Short‐faced lineage then reached the continent and subsequently expanded its range and diversified into the four extant genera. Among bats, independent lineages of aerial insectivores and nectarivores have also recolonized the continent after evolving in the West Indies. The evidence for an insular origin of the short‐faced frugivorous radiation completes a dynamic model of Caribbean biogeography that encompasses an entire biological community.

The traditional explanation of the distribution of the Mormoopidae is that this family originated in southern Central America or northern South America, later expanding its range north to Mexico and the West Indies, and differentiating into eight species. An alternative fossil-based hypothesis argues that the family originated in the northern Neotropics, reached the Caribbean early in its history, and dispersed to South America after the completion of the Isthmus of Panama. The present study analyses new and previously published sequence data from the mitochondrial 12S, tRNAval, 16S, and cytochrome b, and the nuclear Rag2, to evaluate species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b often coincide with published morphological characters and show that the family contains at least 13 species. Two additional, morphologically indistinct, lineages are restricted to Suriname and French Guiana. Phylogeny-based inferences of ancestral area are equivocal on the geographical origin of mormoopids, in part because several internal nodes are not resolved with the available data. Divergences between Middle American and Antillean populations are greater than those between Mexico/Central America and South America. This suggests that mormoopids diversified in northern Neotropics before entering South America. A northern neotropical origin for mormoopids is congruent with both the Tertiary fossil record and recent phylogenetic hypotheses for the sister family to the Mormoopidae, the Phyllostomidae.

Two assumptions have framed previous systematic and biogeographic studies of the family Natalidae: that it comprises a few widespread species, and that extant lineages originated in Mexico and/or Central America. This study analyzes new sequence data from the mitochondrial cytochrome b and the nuclear Rag2, to clarify species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b coincide with published morphological characters, and show that the family includes at least eight species. One newly recognized species is known to live from a single locality in Jamaica, suggesting immediate conservation measures and underscoring the urgency of taxonomic revision. Among the three genera, Chilonatalus and Natalus form a clade, to the exclusion of Nyctiellus. This phylogeny and the geographic distribution of natalids, both extant and extinct, are hardly compatible with a Middle American origin for the group. Instead, extant natalids appear to have originated in the West Indies. The threat of Caribbean hurricanes early in their evolutionary history might account for the specialized cave roosting that characterizes all natalids, even continental species.

A combination of 1,140 base pairs of the mitochondrial cytochrome b gene of Platalina, Lionycteris, and several species of Lonchophylla (Chiroptera: Phyllostomidae) with 150 morphological, sex chromosome, and restriction site characters were used in an attempt to resolve relationships among the lonchophylline taxa. In addition, the monophyly of Lonchophylla was tested, particularly with respect to Platalina. The most parsimonious hypothesis of relationships using all available characters was (L. mordax ((L. chocoana (L. robusta, L. handleyi))(L. thomasi (Lionycteris, Platalina)))). Lonchophylla appears to be paraphyletic, but this arrangement is not well supported. Our analyses suggest that Platalina is not simply a large Lonchophylla, as had been suggested by previous morphological analyses. The low support values for basal relationships found in this study are probably caused by saturation in cytochrome b 3rd positions. Additionally, 2 alternative explanations are viable (if improbable): unsampled lonchophyllines are necessary to confidently resolve relationships at the base of the group, or the lack of resolution at the base of the lonchophylline phylogeny might be explained by rapid speciation following the separation from other glossophagines. Future work examining the phylogenetic relationships of lonchophylline bats should focus on describing new taxa, obtaining tissue samples from unsequenced representatives, and adding nuclear loci to this mitochondrial DNA data set.

Vicariance and dispersal hypotheses have been proposed over the last two hundred years to explain the distribution, diversity, and faunal composition of the Caribbean biota. Despite great advances in understanding the geological history of the region, recent biogeographical reviews have not used historical biogeographical methods. In this paper I review the taxonomy, distribution and phylogeny of all Cenozoic Caribbean non-volant mammals and four bat lineages, and present reconciled trees for available phylogenies. Dates available from the fossil record and hypotheses of divergence based on molecular phylogenetic studies are also included in general assessments of fit between proposed geological models and Caribbean mammal diversification. The evidence posited in mammalian phylogenies does not add to the argument of dispersal vs. vicariance. One previously unidentified temporal pattern, the colonization of the Caribbean by South American mammals between the Palaeocene and the Middle Miocene, accounts for the distribution and phylogeny of the majority of lineages studied. Choloepodine and megalocnine sloths, hystricognath rodents, and primates all arrived during this window of colonization. Of these, megalocnine sloths, hystricognath rodents, Brachyphylla and allied bats, Stenodermatina bats, and primates fit the pattern of divergence from the mainland implied by the Gaarlandia hypothesis. Sloths, rodents and primates also roughly fit the timing of arrival to the Caribbean implied by Gaarlandia. The remaining taxa show contradictory dates of divergence according to molecular clock estimates, and no taxa fit the predicted timing and pattern of divergence among Antillean landmasses under the Gaarlandia model. Choloepodine sloths, murid rodents, insectivorans, mormoopids, and natalids show patterns of divergence from the mainland that are inconsistent with the Gaarlandia hypothesis and seem to require taxon-specific biogeographical explanations.