Species richness under a vertebral stripe: integrative taxonomy uncovers three additional species of Pholidobolus lizards (Sauria, Squamata, Gymnophthalmidae) from the north-western Colombian Andes.

The systematic study of biodiversity underlies appropriate inference in most other fields of biological research, yet it remains hampered by disagreements on both theoretical and empirical issues such as the species concept and the operational diagnosis of a species. Both become particularly challenging in those lineages where morphological traits are evolutionarily constrained by their adaptive value. For instance, cryptic organisms often conserve or converge in their external appearance, which hinders the recognition of species boundaries. An integrative approach has been adopted to study microgeographic variation in the leaf-litter lizard Pholidobolusvertebralis and test three predictions derived from the evolutionary species concept. Molecular data provided unambiguous evidence of divergence among the three recovered new clades and a common evolutionary history for each of them. The broadly sympatric clades were indeed diagnosable from externally visible traits, such as head scales, adult size, and sexually dimorphic ventral colouration. Also, they barely overlapped on the phenotypic space that summarised 39 morphometric and meristic traits. These clades are described as three species and an available name is suggested for a recovered fourth clade. The geographic distribution of the new and proximate species suggests a role for elevation on evolutionary divergence; it also raises interesting questions on the speciation pattern of an otherwise underestimated cryptic lineage.

A new species of Pristimantis (Anura: Strabomantidae) with a colourful venter from the cloud forests of Colombian western Andes.

The Terrarana frogs of the genus Pristimantis are acknowledged for their direct development into froglets and for their astonishing species richness, which renders it the anuran genus with the highest number of species. We describe a new species of Pristimantis from the northwestern Andes of Colombia. The species is distributed from an area between 2750-2900 m.a.s.l. in the Mesenia-Paramillo Nature Reserve. Pristimantis postducheminorum sp. nov. differs from other, phylogenetically related, or similar resembling Pristimantis taxa by a striking yellow coloration in the ventral area, dark grey coloration in the concealed surfaces of the thighs and groin, absence of nuptial pads, presence of lateral fringes on fingers, presence of vomerine odontophores triangular in shape from the ventral view, and absence of dorsolateral folds. Molecular phylogenetics place this new species close to P. satagius and therefore within the P. ridens species group. The new species is also phylogenetically close and sympatric with the recently described P. ferwerdai, which further indicates that the Pristimantis fauna has been notoriously underestimated in the Colombian western cloud forests, a fact that should be considered in assessments of environmental impact.

Molecular systematics and genital morphology of the Neotropical cockroaches from the genus Xestoblatta (Blattellidae).

The Neotropics harbors a tremendous diversity of cockroaches yet their evolutionary history is largely unknown. We reconstructed for the first time the phylogeny of the Neotropical genus Xestoblatta Hebard using mitochondrial and nuclear genes from 12 species distributed in Central America and northern South America. Additionally, we conducted a morphological analysis of external characters and male genitalia. In the phylogenetic analysis we recovered the genus Xestoblatta as non-monophyletic, resulting in three unrelated lineages. From the morphological variability described here, we identified three different morphological groups matching the phylogenetic results. The phylogenetic relationships of the three lineages within the Blattellidae were partially resolved. Lineage 1 was nested within a supported clade corresponding to the tribes Blattellini + Symplocini, while lineages 2 and 3 nested within the clade corresponding to the tribe Pseudomopini. Based on our results, we propose to divide Xestoblatta (sensu lato) into three monophyletic genera: Antroxestoblatta gen.n., Sinatablatta gen.n., and Xestoblatta (sensu stricto). We also describe a new species Sinatablatta magdalenensis sp.n. and propose a taxonomic rearrangement for Xestoblatta (sensu lato).

Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation.

Cryptosporidium is a leading cause of waterborne outbreaks globally, and Cryptosporidium hominis and C. parvum are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages.

Out of the blue: A new rain frog species of the genus Pristimantis (Anura: Craugastoridae) from the northern Cordillera Central in Colombia.

Continuous sampling in well studied areas may lead to new amphibian species discoveries, because population dynamics allow rare species to go unnoticed for years. Based on recent sampling of frogs in the northeastern region of Colombia, here we provide genetic, morphological, and bioacoustics evidence to support the description of a new species of the genus Pristimantis. Phylogenetic analysis suggests the new species is a member of the P. lacrimosus species group, a clade of 25 species that is highly diverse in Ecuador and Peru. This new species is more closely related to allopatric species from Peru and Guyana (i.e. P. olivaceus, P. pluvialis, P. pulchridormientes, and an undetermined Pristimantis). The new species has green-yellow coloration and a remarkable brown interocular band, which is unusual in the genus and which inspired the epithet. Pristimantis zorro sp. nov. has only been found at one locality at 1860 m s.a.l., on the eastern flank of the northern Cordillera Central in Department of Antioquia, Colombia. The new species inhabits the ecotone between the humid cloud forest and open areas. Repeated visits to the type locality suggest high variation in population abundance and/or species detection, because we have occasionally observed many individuals in briefs periods of times. In addition, we discuss the biogeographical and systematic implications of our species discovery.

A new species of Pristimantis (Anura: Craugastoridae) from the cloud forests of Colombian western Andes.

The frogs of the genus Pristimantis are recognized for their characteristic reproductive mode and for their incredible diversity of species, becoming the genus with the highest number of species within tetrapod vertebrates. We describe here a new species of Pristimantis from the northwestern Andes of Colombia. The species was found between 2000-2500 m.a.s.l., mostly within moss hanging of tree branches in a tropical cloud forest. It can be easily distinguished from other Pristimantis species of the western Andes by the unique black and white patterning in the ventral surface and the flanks, the hourglass-shaped dorsal folds, and the prominent conical tubercles on eyelids, heels, and outer edge of tarsus. A phylogenetic analysis further supports its status of a lineage reciprocally monophyletic to P. satagius and separated by a genetic distance of 0.03; the latter species bear whitish rather than predominantly black ventral coloration. To the best of our knowledge, this species is only known from the 2,500 ha nature reserve Mesenia-Paramillo, despite other research on this area of the country. Therefore, the species is declared vulnerable while new evidence on its distribution range is accumulated.

Genomic Basis of Convergent Island Phenotypes in Boa Constrictors.

Convergent evolution is often documented in organisms inhabiting isolated environments with distinct ecological conditions and similar selective regimes. Several Central America islands harbor dwarf Boa populations that are characterized by distinct differences in growth, mass, and craniofacial morphology, which are linked to the shared arboreal and feast-famine ecology of these island populations. Using high-density RADseq data, we inferred three dwarf island populations with independent origins and demonstrate that selection, along with genetic drift, has produced both divergent and convergent molecular evolution across island populations. Leveraging whole-genome resequencing data for 20 individuals and a newly annotated Boa genome, we identify four genes with evidence of phenotypically relevant protein-coding variation that differentiate island and mainland populations. The known roles of these genes involved in body growth (PTPRS, DMGDH, and ARSB), circulating fat and cholesterol levels (MYLIP), and craniofacial development (DMGDH and ARSB) in mammals link patterns of molecular evolution with the unique phenotypes of these island forms. Our results provide an important genome-wide example for quantifying expectations of selection and convergence in closely related populations. We also find evidence at several genomic loci that selection may be a prominent force of evolutionary change-even for small island populations for which drift is predicted to dominate. Overall, while phenotypically convergent island populations show relatively few loci under strong selection, infrequent patterns of molecular convergence are still apparent and implicate genes with strong connections to convergent phenotypes.

A morphological database for Colombian anuran species from conservation-priority ecosystems.

Species traits provide a strong link between an organism's fitness and processes at community and ecosystem levels. However, such data remain scarce for amphibians in the Neotropics. Colombia is the country with the highest number of threatened amphibians and the second greatest number of amphibian species worldwide. We present a data set containing eight morphological traits for 4,623 museum specimens of the seven largest collections in the country corresponding to 293 species of 14 families. The number of measured specimens per species ranged from 1 to 118 individuals with a median of 8 individuals per species. Overall, this database gathered morphological information for 37.6% of Colombian anuran diversity. Species measured were mainly distributed in the high Andean forest, the páramo, and wetland ecosystems, and was part of a national initiative led by the Instituto Alexander von Humboldt. The morphological traits were selected on the basis of their role in species' responses to environmental variability and their contributions to ecosystem processes. These traits were related to habitat use, (forearm length, tibia length, femur length, foot length, and foot webbing), predation and food chains (head width and mouth width), and nutrient recycling (snout-vent length). We expect this data set will be used in studies on functional diversity in amphibians and the development of conservation planning for these taxa. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

Getting better temporal and spatial ecology data for threatened species: using lightweight GPS devices for small primate monitoring in the northern Andes of Colombia.

The use of GPS telemetry has been a reliable research tool for the study of primate biology in recent years. Although in the past technological restrictions limited its use mainly to large primates, recent improvements in battery size make it possible to use this technology for small species. We used GPS devices for monitoring two adult white-footed tamarins (Saguinus leucopus) from a free-ranging group, and assessed its applicability for recording spatial and ecological data. GPS devices were operational for 66 and 85 days, recording 221 positions (36.6% acquisition rate; 73% of which were highly accurate) and 3195 activity values for both individuals. Depending on the estimation method, we calculated the home range size for the group to be 19.4 and 22.9 ha, which were within the range for the species in other localities. The animals were active each day for 11 h, with high activity during the early morning. The monkeys showed a constant and alternate use of four sleeping sites with a limited reuse of the same site on consecutive nights. These daily activity and sleeping site use patterns are similar to those reported for other Saguinus species. Based on the kind and quality of the data recorded, we consider GPS telemetry to be an efficient and advantageous method for tracking and obtaining ecological information from S. leucopus. In comparison to other data collection methods, GPS telemetry required fewer personnel and less time commitment to record data without compromising the accuracy of the spatial and activity information we obtained.

A new species of Leucostethus (Anura: Dendrobatidae) from the eastern versant of the Central Cordillera of Colombia and the phylogenetic status of Colostethus fraterdanieli.

We describe a new species of Dendrobatidae from the eastern flank of the northern Central Cordillera in Colombia and assign it to the recently named genus Leucostethus. We also assess the phylogenetic status of the Colostethus fraterdanieli "complex" which according to our phylogenetic inference, is closely related to the new species. We use morphological, genetic and bioacoustic evidence to describe the new species and to expand the phylogeny of the genus Leucostethus. As a result, we transfer the content of C. fraterdanieli "complex" to Leucostethus. The new species differs from the Leucostethus fraterdanieli "complex" species by having white testes, straight pale ventrolateral stripes and high genetic divergence (17% in Cyt-b). According to our results, the genus Leucostethus is distributed in the western Amazonia from Ecuador and Peru, and both the northern Andes and Pacific lowlands in Colombia. We also found that L. fraterdanieli sensu stricto is restricted from mid (1600 m.a.s.l) to high (2500 m.a.s.l) elevation on the northern Central Cordillera in Antioquia. Extensive geographic sampling and more thorough morphological and bioacoustic examination need to be considered to solve the genetic clusters observed in the Leucostethus fraterdanieli "complex".

Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE).

The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species' distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus.

Phylogenetic analysis of the Neotropical Pristimantis leptolophus species group (Anura: Craugastoridae): molecular approach and description of a new polymorphic species.

Pristimantis, distributed throughout the New World tropics, is the most speciose vertebrate genus. Pristimantis presents an enormous morphological diversity and is currently divided into several demonstrably non-monophyletic phenetic species groups. With the purpose of increasing our understanding of Pristimantis systematics, we present the first phylogenetic analysis using molecular evidence to test the monophyly and infer evolutionary relationships within the Pristimantis leptolophus group, an endemic group of frogs from the highlands of the Colombian Andes. Our phylogenetic reconstruction recovers the group as monophyletic with high support, indicating general concordance between molecular data and morphological data. In addition, we describe a new polymorphic species lacking conspicuous tubercles, a regular attribute among species of the P. leptolophus species group and endemic from the Páramo de Sonsón complex (Antioquia, Colombia). The phylogenetic position of the new species is inferred and other systematic implications in the light of our results are discussed.

Out of Amazonia: the unexpected trans-Andean distribution of Cochranella resplendens (Lynch and Duellman, 1978) (Anura: Centrolenidae).

The glassfrog genus Cochranella, with nine recognized species, is distributed in the lowlands and mid elevation of the Neotropical forests, from Nicaragua to Bolivia (Guayasamin et al. 2009; Twomey et al. 2014). Four species are trans-Andean-C. granulosa (Taylor 1949) occurs in the lowlands and mountains, at mid elevation, of Central America, C. litoralis (Ruiz-Carranza & Lynch 1996) and C. mache Guayasamin & Bonaccorso 2004 occur in the Pacific lowlands and the western cloud forests of Colombia and Ecuador, and C. euknemos (Savage & Starrett 1967) occurs both in Central America and South America (northwestern Colombia).-The other five species have cis-Andean distributions in the Amazonian slopes and lowlands, from Colombia to Bolivia: C. nola Harvey 1996, C. guayasamini Twomey, Delia & Castroviejo-Fisher 2014, C. resplendens (Lynch & Duellman 1973), C. erminea Torres-Gastello, Suárez-Segovia & Cisneros-Heredia 2007, and C. phryxa Aguayo-Vedia & Harvey 2006. In Colombia, C. resplendens is known from the foothills of the Amazon versant in Caquetá (Malambo et al. 2013) and Putumayo (Lynch & Duellman 1973; Ruiz-Carranza et al. 1996). The species is also known from Ecuador (Lynch & Duellman 1973) and Peru (Twomey et al. 2014). Here, we report two new records of Cochranella resplendens, extending the species distribution beyond the Amazonian lowlands into the northern Cordillera Central in Colombia.

The collection of the Herpetological Museum of the University of Antioquia (northwestern Colombia).

Northwestern South America harbors one of the richest herpetofauna in the world. The connection among several biogeographic provinces along with climatic and orographic complexity makes this region an important contributor to the Neotropical biodiversity. Despite of this importance, the amphibian and reptile fauna in this area remains largely unknown as few herpetological collections has been made in recent decades. Motivated by this, the Herpetological Museum at the Universidad de Antioquia (Medellín, Colombia) has been increasing the collection in the last 16 years to better understand the herpetofaunal diversity and thus contribute to ecological, systematic, biogeographic and conservation research in the Neotropics. Here, we present the results of this effort and highlight how future collection will impact our understanding of the Neotropical herpetofauna.

A new colorful species of Pristimantis (Anura: Craugastoridae) from the eastern flank of the Cordillera Central in Colombia .

We describe a new species of Pristimantis from the humid forests on the eastern flank of the northern Cordillera Central in Colombia (6º 23' 19.3554" N, 75º 1' 24.0594" W; ca. 1150 m.a.s.l.). Pristimantis jaguensis sp. nov. is characterized by an extraordinary variation in color and is readily distinguished from congeneric species by lacking nuptial pads, discoidal fold and conical calcar tubercles; flanks and belly white to cream without blotches as well as iris yellow ocher to copper with thick brown reticulation and cream sclera. Molecular phylogenetic analyses recovered the new species in a clade with species mostly distributed in Ecuador. Our finding suggests that new taxa can still be discovered in the Middle Magdalena River valley of Colombia despite the extensive sampling this region has received during the last decades. 

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica.

Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests--among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.

A new red-eyed treefrog of Agalychnis (Anura: Hylidae: Phyllomedusinae) from middle Magdalena River valley of Colombia with comments on its phylogenetic position.

We describe a new species of the charismatic red-eyed treefrogs (genus Agalychnis) from middle Magdalena River valley of Colombia (05°50'8.04"N, 74°50'16.55"W, 380 m a.s.l.). The new species is readily distinguished from all species members of the group by having orange flanks with small white warts. Phylogenetic analysis of DNA sequences of 16S rRNA gene recovered the new species as a member of the Agalychnis callidryas group. The presence of a red hue in the iris and a golden reticulated palpebral membrane, putative synapomorphies of the clade, support this hypothesis. Our analysis suggests that Agalychnis terranova sp. nov is closely related to A. callidryas from Central America and is proposed as its sister species with an uncorrected genetic distance of 5.69% between these taxa. The phylogenetic position and the geographic distribution of the new taxon add new lights to the presence of a biogeographic disjunction between Middle America lowlands, the Pacific region and Magdalena River valley of Colombia.