DNA barcoding of Jamaican bats: implications to Neotropical biodiversity

<p>We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study.</p

Analysis of bat humeri from Late Pleistocene Talara Tar Seeps of northwestern Peru, with paleoenvironmental implications

<p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at <a href="http://www.tandfonline.com/UJVP" target="_blank">www.tandfonline.com/UJVP</a></p> <p>Citation for this article: Moretto, L., B. K. Lim, R. Cadenillas, and J.-N. Martinez. 2016. Analysis of bat humeri from Late Pleistocene Talara Tar Seeps of northwestern Peru, with paleoenvironmental implications. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1250097.</p

Supplementary Material from The role of ecological factors in shaping bat cone opsin evolution

Bats represent one of the largest and most striking nocturnal mammalian radiations, exhibiting many visual system specializations for performance in light-limited environments. Despite representing the greatest ecological diversity and species richness in Chiroptera, Neotropical lineages have been undersampled in molecular studies, limiting the potential for identifying signatures of selection on visual genes associated with differences in bat ecology. Here, we investigated how diverse ecological pressures mediate long-term shifts in selection upon long-wavelength (<i>Lws</i>) and short-wavelength (<i>Sws1</i>) opsins, photosensitive cone pigments that form the basis of colour vision in most mammals, including bats. We used codon-based likelihood clade models to test whether ecological variables associated with reliance on visual information (e.g. echolocation ability and diet) or exposure to varying light environments (e.g. roosting behaviour and foraging habitat) mediated shifts in evolutionary rates in bat cone opsin genes. Using additional cone opsin sequences from newly sequenced eye transcriptomes of six Neotropical bat species, we found significant evidence for different ecological pressures influencing the evolution of the cone opsins. While <i>Lws</i> is evolving under significantly lower constraint in highly specialized high-duty cycle echolocating lineages, which have enhanced sonar ability to detect and track targets, variation in <i>Sws1</i> constraint was significantly associated with foraging habitat, exhibiting elevated rates of evolution in species that forage among vegetation. This suggests that increased reliance on echolocation as well as the spectral environment experienced by foraging bats may differentially influence the evolution of different cone opsins. Our study demonstrates that different ecological variables may underlie contrasting evolutionary patterns in bat visual opsins, and highlights the suitability of clade models for testing ecological hypotheses of visual evolution

Convergent evolution of the <i>CRX</i> gene in bats based on a tree derived from the Bayesian analysis of nucleotide sequences.

<p>Numbers and symbols above the branches are the positions and amino acid replacements. Sequences at the internal nodes were reconstructed by the Maximum Likelihood method in PAML.</p

Convergent evolution of the <i>SAG</i> gene in bats based on a tree derived from the Bayesian analysis of nucleotide sequences.

<p>Numbers and symbols above the branches are the positions and amino acid replacements. Sequences at internal nodes were reconstructed by the Maximum Likelihood method in PAML.</p

Table S1 from The role of ecological factors in shaping bat cone opsin evolution

Species list, accession number and ecological classificatio

Table S8 from The role of ecological factors in shaping bat cone opsin evolution

Codon-based estimates of divergence between bat Lws and Sws1 sequence

Table S8 from The role of ecological factors in shaping bat cone opsin evolution

Codon-based estimates of divergence between bat Lws and Sws1 sequence

Table S1 from The role of ecological factors in shaping bat cone opsin evolution

Species list, accession number and ecological classificatio

Nuclear and mtDNA phylogenetic analyses clarify the evolutionary history of two species of native Hawaiian bats and the taxonomy of Lasiurini (Mammalia: Chiroptera)

<div><p>Previous studies on genetics of hoary bats produced differing conclusions on the timing of their colonization of the Hawaiian Islands and whether or not North American (<i>Aeorestes cinereus</i>) and Hawaiian (<i>A</i>. <i>semotus</i>) hoary bats are distinct species. One study, using mtDNA COI and nuclear Rag2 and CMA1, concluded that hoary bats colonized the Hawaiian Islands no more than 10,000 years ago based on indications of population expansion at that time using Extended Bayesian Skyline Plots. The other study, using 3 mtDNA and 1 Y-chromosome locus, concluded that the Hawaiian Islands were colonized about 1 million years ago. To address the marked inconsistencies between those studies, we examined DNA sequences from 4 mitochondrial and 2 nuclear loci in lasiurine bats to investigate the timing of colonization of the Hawaiian Islands by hoary bats, test the hypothesis that Hawaiian and North American hoary bats belong to different species, and further investigate the generic level taxonomy within the tribe. Phylogenetic analysis and dating of the nodes of mtDNA haplotypes and of nuclear CMA1 alleles show that <i>A</i>. <i>semotus</i> invaded the Hawaiian Islands approximately 1.35 Ma and that multiple arrivals of <i>A</i>. <i>cinereus</i> occurred much more recently. Extended Bayesian Skyline plots show population expansion at about 20,000 years ago in the Hawaiian Islands, which we conclude does not represent the timing of colonization of the Hawaiian Islands given the high degree of genetic differentiation among <i>A</i>. <i>cinereus</i> and <i>A</i>. <i>semotus</i> (4.2% divergence at mtDNA Cytb) and the high degree of genetic diversity within <i>A</i>. <i>semotus</i>. Rather, population expansion 20,000 years ago could have resulted from colonization of additional islands, expansion after a bottleneck, or other factors. New genetic data also support the recognition of <i>A</i>. <i>semotus</i> and <i>A</i>. <i>cinereus</i> as distinct species, a finding consistent with previous morphological and behavioral studies. The phylogenetic analysis of CMA1 alleles shows the presence of 2 clades that are primarily associated with <i>A</i>. <i>semotus</i> mtDNA haplotypes, and are unique to the Hawaiian Islands. There is evidence for low levels of hybridization between <i>A</i>. <i>semotus</i> and <i>A</i>. <i>cinereus</i> on the Hawaiian Islands, but it is not extensive (<15% of individuals are of hybrid origin), and clearly each species is able to maintain its own genetic distinctiveness. Both mtDNA and nuclear DNA sequences show deep divergence between the 3 groups (genera) of lasiurine bats that correspond to the previously recognized morphological differences between them. We show that the Tribe Lasiurini contains the genera <i>Aeorestes</i> (hoary bats), <i>Lasiurus</i> (red bats), and <i>Dasypterus</i> (yellow bats).</p></div