Optimization of Genotype by Sequencing data for phylogenetic purposes.

• Herein we propose a framework for assembling and analyzing Genotype by Sequencing (GBS) data to better understand evolutionary relationships within a group of closely related species using the mastiff bats (Molossus) as our model system. Many species within this genus have low-levels of genetic variation within and between morphologically distinct species, and the relationships among them remain unresolved using traditional Sanger sequencing methods. Given that both de novo and reference genome pipelines can be used to assemble next generation sequences, and that several tree inference methodologies have been proposed for single nucleotide polymorphism (SNP) data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Different alignments and phylogenetic inferences produced consistent results, supporting the GBS approach for answering evolutionary questions on a macroevolutionary scale when the genetic distance among phenotypically identifiable clades is low. We highlight the importance of exploring the relationships among groups using different assembly assumptions and also distinct phylogenetic inference methods, particularly when addressing phylogenetic questions in genetic and morphologically conservative taxa. • The method uses the comparison of several filter settings, alignments, and tree inference approaches on Genotype by Sequencing data. • Consistent results were found among several approaches. • The methodology successfully recovered well supported species boundaries and phylogenetic relationships among species of mastiff bats not hypothesized by previous methods.

DNA barcoding and genetic diversity of phyllostomid bats from the Yucatan Peninsula with comparisons to Central America.

The mitochondrial cytochrome c oxidase subunit I gene is the standard DNA barcoding region used for species identification and discovery. We examined the variation of COI (454 bp) to discriminate 20 species of bats in the family Phyllostomidae that are found in the Yucatan Peninsula of southeastern Mexico and northern Guatemala and compared them genetically to other samples from Central America. The majority of these species had low intraspecific variation (mean = 0.75%), but some taxa had intraspecific variation ranging to 8.8%, suggesting the possibility of cryptic species (i.e. Desmodus rotundus and Artibeus jamaicensis). There was a recurring biogeographic pattern in eight species with a separation of northern and southern Middle American localities. The Yucatan Peninsula was a discrete area identified in four species, whereas Panama was recovered in five species of phyllostomid bats. Our study establishes a foundation for further molecular work incorporating broader taxonomic and geographic coverage to better understand the phylogeography and genetic diversity that have resulted from the ecological constraints in this region and the remarkable differentiation of bats in the Neotropics.

Cytogenetics of collared lemmings (Dicrostonyx groenlandicus). II. Meiotic behavior of B chromosomes suggests a Y-chromosome origin of supernumerary chromosomes.

The patterns of synapsis and chiasma formation of the B chromosomes of male collared lemmings (Dicrostonyx groenlandicus) were analyzed by light and electron microscopy and compared to expectations for various hypotheses for the intragenomic origin of supernumerary chromosomes. Pachytene analysis revealed a variety of synaptic configurations including B-chromosome univalents, bivalents and trivalents. In approximately one-half of the pachytene nuclei examined, B chromosomes were in synaptic associations with the normally unpaired portion of the Y chromosome. The B-chromosome configurations at pachynema, including those involving the Y chromosome, were maintained into diakinesis and metaphase I. The meiotic behavior of the B chromosomes was inconsistent with their derivation from centric-fusion products, isochromosome formation, small-autosome polysomy, or the X chromosome. However, the frequent synapsis and apparent recombination between B chromosomes and the Y chromosome implicate this sex chromosome as a possible source of the B chromosomes in collared lemmings.

Cytogenetics of collared lemmings (Dicrostonyx groenlandicus). I. Meiotic behavior and evolution of the neo-XY sex-chromosome system.

Electron-microscopic analysis of surface-spread synaptonemal complexes at pachynema and light-microscopic analysis of chromosomal configurations at diakinesis/metaphase I corroborate the hypothesized neo-XY derivation of the sex chromosomes of Dicrostonyx groenlandicus. Although an intact neo-XY pairing configuration was observed in a relatively small percentage of the pachytene cells in each individual, the high incidence of neo-XY bivalents at diakinesis/metaphase I suggests that the other observed pachytene configurations were artifacts of the physical stresses of the surface-spreading procedure. The very low frequency (0.6%) of univalent neo-X and neo-Y chromosomes at diakinesis and metaphase I is attributable to consistent synapsis and recombination between their homologous autosomally derived segments. The resultant stability of the sex bivalent through metaphase I may have increased the efficacy of sex-chromosome segregation, and thereby played a mechanistic role in the evolutionary incorporation of the neo-XY sex-chromosome constitution in D. groenlandicus.

Cytogenetic nomenclature of deer mice, Peromyscus (Rodentia): revision and review of the standardized karyotype. Report of the Committee for the Standardization of Chromosomes of Peromyscus.

A revision of the standardized karyotype of deer mice (Peromyscus) is presented. This revision addresses short-comings of the original standardization, contains a substantial increase in the number of G-band markers and provides a nomenclature for the G-bands of each autosome and the X chromosome. Using the revised standardized karyotype, we specify the particular G-bands or patterns that identify each chromosome and catalog the more problematic chromosome identifications and likely misidentifications. For each chromosome, we present an overview of previously reported variation in euchromatic arrangement and heterochromatic constitution. We then review previous applications of the standardized karyotype and summarize the predominant findings from cytogenetic and cytosystematic studies of Peromyscus and related taxa.