PHYLOGENETIC RELATIONSHIPS OF MORMOOPID BATS (CHIROPTERA: MORMOOPIDAE) BASED ON MORPHOLOGICAL DATA

Acoustic clue: bringing echolocation call data into the distribution dilemma of Pteronotus (Chiroptera: Mormoopidae) complexes in Central America

In Central America, the distributional limits and the contact zones of some Pteronotus species, such as the naked-backed bats and the lesser mustached bats, are unclear. To elucidate the distributional dilemma of the species groups Pteronotus fulvus + Pteronotus davyi and Pteronotus psilotis + Pteronotus personatus in Central America, we studied the acoustic variation of their echolocation calls along the range of possible contact zones and the existence of distinct phonic groups. We performed hierarchical k-means clustering on principal components (HCPC) using acoustic samples from Mexico, Honduras, El Salvador, Nicaragua and Costa Rica to describe the global acoustic diversity, possibly overlooking differences between species groups. We assessed whether those acoustic differences were related to the geographical distance and geographical location. We found evidence of sympatry for three phonic groups within each species complex, without a clear correspondence to the known distribution of species. The changes in frequency of their echolocation calls seem to follow a similar pattern to the geographical variation in body size of the species. Future studies in Central America should include an integrative sampling of individually captured, tagged and recorded bats to help in resolution of the distribution dilemma raised here.

Genetic Introgression and Morphological Variation in Naked-Back Bats (Chiroptera: Mormoopidae: Pteronotus Species) along Their Contact Zone in Central America

Two sibling bare-backed bat species (Pteronotus fulvus and P. gymnonotus) have been traditionally differentiated by their size. However, intermediate specimens between the two species have been found in sympatric populations along southern Mexico and it has been suggested that they may be the outcome of a hybridization process between the two species. We used one mitochondrial (COI), three nuclear markers (PRKCL, STAT5A and RAG2) and 13 microsatellites to explore the evolutionary relationships between these two species and elucidate whether the intermediate morphotypes correspond to hybrid individuals. These markers have been analyzed in sympatric and allopatric populations of the two species plus the closely related species Pteronotus davyi. We confirmed the species-level differentiation of the three lineages (P. fulvus, P. davyi and P. gymnonotus), but the phylogenetic hypotheses suggested by the nuclear and mitochondrial markers were discordant. We confirm that the discordance between markers is due to genetic introgression through the mitochondrial capture of P. fulvus in P. gymnonotus populations. Such introgression was found in all P. gymnonotus specimens across its sympatric distribution range (Mexico to Costa Rica) and is related to expansion/retraction species distribution pulses associated with changes in forest distribution during the Quaternary climate cycles. Microsatellite analyses showed contemporary genetic contact between the two sympatric species and 3.0% of the samples studied were identified as hybrids. In conclusion, we found a historical and asymmetric genetic introgression (through mitochondrial capture) of P. fulvus into P. gymnonotus in Mexico and Central America and a limited contemporary gene exchange between the two species. However, no relationship was found between hybridization and the intermediate-sized specimens from southern Mexico, which might likely result from a clinal variation with latitude. These results confirm the need for caution when using forearm size to identify these species in the field and when differentiating them in the laboratory based on mitochondrial DNA alone.

Comparative morphology and scaling of the femur in yangochiropteran bats

Better known by their remarkable forelimb morphology, bats are also unique among mammals with respect to their hindlimbs. Their legs are rotated through 180°, generally reduced in size, and in some extant taxa particular bones (e.g. fibula) can even be absent. The femur is the main leg bone, but to date few bat studies have considered its morphology in detail, none in a wide-scale comparative study. Yangochiroptera is the largest bat taxon, spans nearly three orders of magnitude in body mass, and is highly diverse both in ecology and behavior, representing a good model for comparative analyses. Here, we describe the anatomy of the femur in a large sample of yangochiropteran bats (125 species, 70 genera, and 12 families), and explore major trends of morphological variation and scaling patterns in this bone. We used 13 categorical characters in the anatomical description and five linear dimensions in the quantitative analyses. Based on the categorical data, each family studied here was diagnosed, and those from the Neotropical region were included in an identification key. From the phylogenetic principal component analysis (pPCA) we showed that, in addition to size, major axes of variation in bat femur are related to robusticity and head morphology, features that are clearly distinct among some families. We also generated a phylomorphospace based on pPCA scores, highlighting convergences in femur shape. Molossidae, Mystacinidae, and Desmodontinae were grouped based on their greater robusticity, a pattern that was also recovered from categorical data. In these families, we found anatomical features (e.g. presence of tubercles and posterior ridges on the greater trochanter, long or medially/distally displaced lateral ridges on the shaft) that are well-known from their functional link with quadrupedal locomotion. Using phylogenetic regressions, we found out that compared with body mass, femur length scaled with negative allometry, as expected, but that femur width scaled isometrically, counter to expectations. As a result, robusticity index (the ratio of width to length), scaled with positive allometry - larger bats tended to have more robust hindlimbs. At species level, our most remarkable finding was related to Myotis simus, which presented the most robust femur (for its size) among yangochiropterans. Our results reinforce the informative potential of the chiropteran femur from both taxonomic and functional perspectives. Furthermore, the allometric trends seen in this bone may help understand the strategies adopted by flying vertebrates to deal with the high energetic cost of flight and, at the same time, evolve diversified foraging behaviors.

Morphology of the axial skeleton of seven bat genera (Chiroptera: Phyllostomidae)

Here we present detailed descriptions and comparisons of the axial skeleton of seven species of bats belonging to five subfamilies of Phyllostomidae of different trophic guilds. The material examined consisted of 34 complete skeletons of seven species. For five of the studied species, previous descriptions have not been conducted, and for the vampires only limited information is available, so that descriptions for these species are here completed. The axial skeleton has characters that allow grouping of the species phylogenetically of the same subfamily and by feeding habits. At the same time, there are characters that associate species from different subfamilies with different types of diet or ways to obtain food.

Gonadal morphogenesis and establishment of the germline in the phyllostomid bat Sturnira lilium

In vertebrates such as the mouse and the human, primordial germ cells (PGCs) arise at the base of the allantois and are carried to the epithelium of the posterior intestine, to later migrate to the primordial gonads. In the case of bats, almost nothing is known about this process. To clarify the dynamics of PGCs during gonadal morphogenesis in the phyllostomid bat Sturnira lilium, the proteins for the Ddx4, Sox9 and Mis genes were detected in the gonads of embryos at different stages of development. We identified 15 stages (St) of embryonic development in Sturnira lilium. We found that the formation of the genital ridge and the establishment of the undifferentiated gonad take place between stages 11 and 14. The onset of morphological differentiation in the gonad is first detected in the male gonads at St17. The first PGCs in meiosis are detected in the ovary at St19, whereas in the testicles, the PGCs were in mitotic arrest. Structural changes leading to testicular and ovarian development in Sturnira lilium are observed to be similar to those described for the mouse; however, differences will be established concerning the time taken for these processes to occur.

Timing and patterns of diversification in the Neotropical bat genus Pteronotus (Mormoopidae)

We investigate the biogeographic processes related to the origin and current patterns of distribution of the extant species of the genus Pteronotus. This clade of insectivorous bats is widely distributed in the Neotropical Region and has recently gone through a taxonomic update which increased more than twice its diversity. Using six molecular markers of 15 Pteronotus lineages ranging from Mexico to Central Brazil, we reconstruct a time-calibrated tree and infer molecular evolutionary rates for this bat genus. In addition, estimates of range evolution across phylogeny were obtained through statistical model testing among six different biogeographic models. The origin of the genus Pteronotus occurred approximately 16million years ago (Ma), with initial cladogenesis events being evenly distributed across the phylogeny. Divergence between most closely related species is recent, falling in the Pleistocene period less than 2.6Ma. Mainland lineages present congruent patterns of north versus south continent splitting while insular clades differ in their time of arrival in the Caribbean Islands. Temporal and geographic range estimates for early nodes of Pteronotus phylogeny suggest a central role of Neogene tectonic reorganizations of Central America in the group diversification process. Also, South American colonization by Pteronotus occurred early in the genus history. Founder-event speciation was an important mode of lineage splitting in Pteronotus, with two independent dispersal jumps having occurred to the Greater Antilles. Finally, Pleistocenic sea-level variation and climatic oscillations are possibly associated with divergence between sister-species and recent ages of MRCA for Pteronotus species.

Sampling diverse characters improves phylogenies: Craniodental and postcranial characters of vertebrates often imply different trees

Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that craniodental characters are significantly more numerous than postcranial characters, but finds no evidence that levels of homoplasy differ in the two partitions. However, a new partition test, based on tree-to-tree distances (as measured by the Robinson Foulds metric) rather than tree length, reveals that relationships inferred from the partitions are significantly different about one time in three, much more often than expected. Such differences may reflect divergent selective pressures in different body regions, resulting in different localized patterns of homoplasy. Most systematists attempt to sample characters broadly across body regions, but this is not always possible. We conclude that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach. We urge the latter.

New insights into the evolution of the Trypanosoma cruzi clade provided by a new trypanosome species tightly linked to Neotropical Pteronotus bats and related to an Australian lineage of trypanosomes

Background

Bat trypanosomes are implicated in the evolution of the T. cruzi clade, which harbours most African, European and American trypanosomes from bats and other trypanosomes from African, Australian and American terrestrial mammals, including T. cruzi and T. rangeli, the agents of the American human trypanosomiasis. The diversity of bat trypanosomes globally is still poorly understood, and the common ancestor, geographical origin, and evolution of species within the T. cruzi clade remain largely unresolved.

Methods

Trypanosome sequences were obtained from cultured parasites and from museum archived liver/blood samples of bats captured from Guatemala (Central America) to the Brazilian Atlantic Coast. Phylogenies were inferred using Small Subunit (SSU) rRNA, glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH), and Spliced Leader (SL) RNA genes.

Results

Here, we described Trypanosoma wauwau n. sp. from Pteronotus bats (Mormoopidae) placed in the T. cruzi clade, then supporting the bat-seeding hypothesis whereby the common ancestor of this clade likely was a bat trypanosome. T. wauwau was sister to the clade T. spp-Neobats from phyllostomid bats forming an assemblage of trypanosome species exclusively of Noctilionoidea Neotropical bats, which was sister to an Australian clade of trypanosomes from indigenous marsupials and rodents, which possibly evolved from a bat trypanosome. T. wauwau was found in 26.5 % of the Pteronotus bats examined, and phylogeographical analysis evidenced the wide geographical range of this species. To date, this species was not detected in other bats, including those that were sympatric or shared shelters with Pteronotus. T. wauwau did not develop within mammalian cells, and was not infective to Balb/c mice or to triatomine vectors of T. cruzi and T. rangeli.

Conclusions

Trypanosoma wauwau n. sp. was linked to Pteronotus bats. The positioning of the clade T. wauwau/T.spp-Neobats as the most basal Neotropical bat trypanosomes and closely related to an Australian lineage of trypanosomes provides additional evidence that the T. cruzi clade trypanosomes likely evolved from bats, and were dispersed in bats within and between continents from ancient to unexpectedly recent times.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-1255-x) contains supplementary material, which is available to authorized users.

The placental mammal ancestor and the post-K-Pg radiation of placentals

To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.

Understanding phylogenetic incongruence: lessons from phyllostomid bats

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

A phylogenetic supertree of the bats (Mammalia: Chiroptera)

We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats Mammalia: Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have locused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades: overall resolution is poor (46.4%, of a fully bifurcating solution) but reaches 100% in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats.