Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul

Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes

Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.

An evaluation of DNA extraction methods on historical and roadkill mammalian specimen

Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.

Complete mitochondrial genome of the Galápagos sea lion, Zalophuswollebaeki (Carnivora, Otariidae): paratype specimen confirms separate species status

The endangered Galápagos sea lion (Zalophuswollebaeki) inhabits the Galápagos Islands off the coast of Ecuador. We present a complete mitochondrial genome (16 465 bp) of a female paratype from the collections of the Natural History Museum Oslo, Norway, assembled from next-generation sequencing reads. It contains all canonical protein-coding, rRNA, tRNA genes, and the D-loop region. Sequence similarity is 99.93% to a previously published conspecific mitogenome sequence and 99.37% to the mitogenome sequence of the sister species Z.californianus. Sequence similarity of the D-loop region of the Z.wollebaeki paratype mitogenome is >99%, while the sequence difference to the Z.californianus sequences exceeds 2.5%. The paratype mitogenome sequence supports the taxonomic status of Z.wollebaeki as a separate species.

Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)

Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.

Museomics and the holotype of a critically endangered cricetid rodent provide key evidence of an undescribed genus

Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.

Complete mitogenomes of Turkish tree squirrels, Sciurus anomalus and S. vulgaris, (Sciuridae: Rodentia: Mammalia) and their phylogenetic status within the tribe Sciurini

The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNA^Ser(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five linegaes of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey' Sciurus holds an important value for revealing evolutionary relationships.

Integrative Taxonomy within Eremias multiocellata Complex (Sauria, Lacertidae) from the Western Part of Range: Evidence from Historical DNA

The Kokshaal racerunner, Eremias kokshaaliensis Eremchenko et Panfilov, 1999, together with other central Asian racerunner species, is included in the Eremias multiocellata complex. In the present work, for the first time, the results of the analysis of historical mitochondrial DNA (barcode) are presented and the taxonomic status and preliminary phylogenetic relationships within the complex are specified. We present, for the first time, the results of the molecular analysis using historical DNA recovered from specimens of several species of this complex (paratypes of the Kokshaal racerunner and historical collections of the Kashgar racerunner E. buechneri from Kashgaria) using DNA barcoding.

Checklist of the mammals (Mammalia) of Colombia

La actualización de la lista de especies presentes en un país es una tarea continua que llena vacíos de información y apoya la toma de decisiones. En los últimos cinco años, ha habido un aumento del número de especies de mamíferos descritas como nuevas en Colombia, así como primeros registros y cambios taxonómicos. Con el fin de actualizar la información de las especies de mamíferos de Colombia, realizamos una revisión exhaustiva de los cambios taxonómicos de las 528 especies registradas en listas previas. Agregamos nuevas especies descritas, así como nuevos registros de especies ya descritas. Discutimos especies cuya presencia ha sido sugerida recientemente en Colombia, pero que no es respaldada por especímenes de museo. La lista actual de mamíferos en Colombia tiene 543 especies, con cuatro descritas en el último año. Esperamos que la lista sea una herramienta apoyar las necesidades de investigación, en especial las extensiones de distribución, los problemas taxonómicos y la conservación de los mamíferos del país. Finalmente, recomendamos que las actualizaciones de la lista sigan estándares nacionales e internacionales como Darwin Core, utilizado por el Repositorio de Información Global sobre Biodiversidad - GBIF, y el Sistema de Información sobre Biodiversidad de Colombia – SiB.

Escaping the nocturnal bottleneck, and the evolution of the dorsal and ventral streams of visual processing in primates

Early mammals were small and nocturnal. Their visual systems had regressed and they had poor vision. After the extinction of the dinosaurs 66 mya, some but not all escaped the 'nocturnal bottleneck' by recovering high-acuity vision. By contrast, early primates escaped the bottleneck within the age of dinosaurs by having large forward-facing eyes and acute vision while remaining nocturnal. We propose that these primates differed from other mammals by changing the balance between two sources of visual information to cortex. Thus, cortical processing became less dependent on a relay of information from the superior colliculus (SC) to temporal cortex and more dependent on information distributed from primary visual cortex (V1). In addition, the two major classes of visual information from the retina became highly segregated into magnocellular (M cell) projections from V1 to the primate-specific temporal visual area (MT), and parvocellular-dominated projections to the dorsolateral visual area (DL or V4). The greatly expanded P cell inputs from V1 informed the ventral stream of cortical processing involving temporal and frontal cortex. The M cell pathways from V1 and the SC informed the dorsal stream of cortical processing involving MT, surrounding temporal cortex, and parietal-frontal sensorimotor domains. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'.

Variation in the Myotis keaysi complex (Chiroptera, Vespertilionidae), with description of a new species from Ecuador

The genus Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Twenty-eight Neotropical species are currently recognized. In this study, we evaluate molecular and morphological variation in the M. keaysi complex, a high elevation clade of Neotropical myotine bats characterized by complex taxonomy and high morphological variation. A phylogeny inferred with cytochrome-b sequences recovered two clades composed of samples traditionally assigned to M. keaysi, with 9% of genetic divergence between them. These clades were also suggested as putative distinct species by molecular species delimitation methods. Qualitative and quantitative morphological analyses indicated a phenotypic discontinuity between specimens from central Andes (including the holotype of M. keaysi) and western lowlands of Ecuador, showing strong congruence between molecular and morphological approaches. We therefore describe a new species for the Tumbes-Choco-Magdalena region, documenting their external and cranial diagnostic characters by comparing them with other Neotropical species. In addition, we provide an emended diagnosis for our new concept of M. keaysi.

San Josecito Cave and Its Paleoecological Contributions for Quaternary Studies in Mexico

San Josecito Cave (2250 m elevation) is located nearby Aramberri, Nuevo León, northeastern Mexico, with excavations occurring in 1935–1941 and 1990. It is a paleontological cave and the significance of its faunal data rests in the understanding of the Quaternary ecosystems of the Mexican Plateau and the Southern Plains. This significance is underpinned by a consideration of associated stratigraphic and geochronological data. The fauna is composed of mollusks, amphibians, reptiles, birds, and mammals. More than 30 extinct vertebrate species have been identified, constituting one of the most important Quaternary localities in the Americas. Radiocarbon dates and faunal correlations indicate the excavated deposits represent an interval of time between 45,000 and 11,000 14C years BP. The current synthesis demonstrates that the previous view of the assemblage as a single local fauna is erroneous and that, instead, several successive local faunas are present within a stratigraphic framework. This finding underscores the need for detailed studies of single localities in building paleoenvironmental models. As a corollary, results point to the necessity of including all vertebrate classes represented from a locality in building those models. In addition, the field and analytical methodologies demonstrate the importance of very detailed paleontological excavations, with precise spatial and temporal controls, to assess the taphonomic history of a locality, construct a stratigraphic and geochronological framework, and infer the paleoecological conditions during the time span considered based on the number of local faunas represented. The recognition of San Josecito Cave as an important Late Pleistocene vertebrate paleontological locality is enhanced with the consideration of its faunal data for paleoenvironment reconstruction and possible contribution to Quaternary paleoclimatic modeling.

A Draft Genome Assembly for the Eastern Fox Squirrel, Sciurus niger

The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly, and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.

First mitochondrial genome of the Caucasian squirrel Sciurus anomalus (Rodentia, Sciuridae)

The Caucasian Squirrel, Sciurus anomalus, is the only representative of the Sciuridae family in the Eastern Mediterranean region. In this study, the mitochondrial genome of the Sciurus anomalus species was generated, and we investigate its phylogenetic position within the Sciuridae family. The generated mitogenome sequence is 16,234 bp. It is composed of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes.

Species richness, geographical affinities and activity patterns of mammals in premontane Andean forests of the Magdalena River basin of Colombia

More than half of the population of Colombia is settled in the Magdalena River basin, resulting in high deforestation rates due to productive activities and urbanisation. Within this scenario of forest loss and ecosystem degradation, it is imperative to record and monitor the biodiversity in order to decrease and mitigate the negative consequences of human activities on species and ecosystems. For six years, we assessed the mammal species richness, abundance and activity patterns in premontane forests of the Magdalena River basin in the Department of Caldas, Colombia. We also presented additional information on the geographical affinities of this fauna. We recorded 101 species, seven of them endemic to Colombia, with Chiroptera being the richest order, followed by Rodentia. Most of the species are common and not listed in threatened categories and only four are vulnerable and two endangered, according to the Red List of the IUCN and the Ministerio de Medio Ambiente y Desarrollo Sostenible of Colombia. The mammalian fauna of the study area is similar to that of other lowland localities in the Neotropics and different to the fauna in highland localities, including the nearby ones. Specifically, this fauna was most similar to that in lowland Tolima and the Caribbean Region of Colombia, Venezuela and Costa Rica; however, when we accounted only for bat fauna, it was more similar to the fauna in Caribbean and Pacific Regions of Colombia. To secure the long-term persistence of these species, we recommend maintenance of the current corridors, such as riparian forests and living fences and an increase in the forested area.

Molecular systematics of the Sicista tianschanica species complex: a contribution from historical DNA analysis

The Tianshan birch mouse Sicista tianschanica is an endemic of the Central Asian mountains and has previously been shown to include several karyomorphs (“Terskey”, “Talgar”, “Dzungar”); however, the taxonomic status of these forms has remained uncertain. We examined the genetic variation in S. tianschanica based on historical DNA samples from museum collections, including the type series. Mitochondrial and nuclear data indicated that the species complex includes two major clades: Northern (N) and Southern (S) (cytb distance 13%). The N clade corresponds to the “Dzungar” karyomorph (Dzungar Alatau, Tarbagatay). The S clade is comprised of four lineages (S1–S4) divergent at 6–8%; the relationships among which are resolved incompletely. The S1 lineage is found in eastern Tianshan and corresponds to the nominal taxon. The S2 is distributed in central and northern Tianshan and corresponds to the “Terskey” karyomorph. The S3 is restricted to Trans-Ili Alatau and belongs to the “Talgar” karyomorph. The S4 is represented by a single specimen from southeastern Dzungar Alatau with "Talgar" karyotype. No interlineage gene flow was revealed. The validity of S. zhetysuica (equivalent to the N clade) is supported. Based on genetic and karyotypic evidence, lineages S2 and S3 are described as distinct species. The status of the S4 requires further investigation.