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Hooper’s deer mouse, Peromyscus hooperi, is the sole member of the Peromyscus hooperi species group. This species is endemic to México where it is restricted to the grassland transition zone in the states of Coahuila, Zacatecas, and San Luis Potosí. Previous studies using mitochondrial and nuclear genes (Cytb, Adh1-I2, Fgb-I7 and Rbp3) did not resolve the phylogenetic relationships of this relatively poorly known species. It was hypothesized that P. hooperi is sister to P. crinitus, and these two taxa are related to P. melanotis, P. polionotus, P. maniculatus, P. keeni, P. leucopus, P. gossypinus, P. eremicus, P. californicus, and Osgoodomys banderanus. Based on morphological characters, karyotypes, and allozymes, P. hooperi does not align with either subgenera Haplomylomys or Peromyscus. However, its unique characteristics (e. g., phallus, karyotype) have been recognized, and therefore it has been retained as its own species group. To better resolve the phylogenetic placement of P. hooperi, we performed target-enrichment and high-throughput sequencing and obtained several thousand nuclear ultraconserved elements and a complete mitogenome from a specimen collected in 1896 by Nelson and Goldman in Coahuila, México. We compared these data with 21 other species of neotomines using genome-wide data. Contrary to previous studies, we found high nodal support for the placement of P. hooperi as sister to a clade that includes Podomys floridanus, Neotomodon alstoni, Habromys simulatus, H. ixtlani, Peromyscus mexicanus, P. megalops, P. melanophrys, P. perfulvus, P. aztecus, P. attwateri, P. pectoralis, and P. boylii. We dated a Pliocene divergence of P. hooperi from its sister group at approximately 3.98 mya, and after the split of P. crinitus at ca. 4.31 mya from other peromyscines. We demonstrated that genome-wide data improve the phylogenetic signal, independently of taxon sampling, for a phylogenetically problematic species such as P. hooperi. We recommend that future genomic studies expand taxon sampling, including members of the subgenus Haplomylomys, to confirm the phylogenetic relationships of P. hooperi and the genetic status of its populations.

Notiosorex is the only genus of shrews in North America with particular adaptations for arid habitats such as deserts. Five species currently are recognized in the genus, one of which, Notiosorex evotis, lives in deciduous rain forest from northern Sinaloa to the state of Jalisco in México. Notiosorex evotis originally was described as a subspecies of N. crawfordi; however, it was recently proposed as a valid species based on a discriminant function analysis of craniodental characters. Morphological differentiation between N. evotis populations and sympatric occurrences with N. crawfordi in northern Sinaloa have been recognized. Here, we used a phylogenetic analysis of a mitochondrial gene (Cytb; 1,140 bp) and the nuclear beta fibrinogen intron 7 (β-fib I7; 385 bp), as well as cranial geometric morphometrics, to assess the taxonomic status of N. evotis. We found sequences of N. evotis forming two main subclades: one that includes the populations of the state of Sinaloa, the other including populations of Nayarit and Jalisco. The boundaries between the two groups seem to be related to the ecotonal cline between the Pacific Lowlands province and the Trans-Mexican Volcanic Belt province, which acts as a geographical barrier. The discriminant function analysis revealed clear differences in skull shape between the three species of Notiosorex to the northwest of its distribution. Considering these multiple lines of evidence from our data set, we confirm that N. evotis is a monotypic species. Our results suggest that geometric morphometrics can be used successfully to identify sibling species by shape, especially in groups where determination by craniodental measurements is not possible.

Species can coexist spatially and temporally by partitioning the niche space and forming complex assemblages made up of different species that share the prey resource. Chiroptera is the second most species-rich mammalian order and about 75% of bat species feed on arthropods, which makes these bats a good model group for studying complex trophic interactions. Next-generation parallel sequencing techniques allow a detailed analysis of arthropod resource partitioning patterns in bats. However, previous studies have not reached a consensus on the concordance between diet composition, habitat use, and segregation of trophic resources in bats. We analyzed diet composition in terms of taxonomy of the insect prey, and the prey characteristics. Feces of 16 bat species were examined in the Mexican Neotropics. We carried out a SIMPER (similarity percentage) test, nonmetric multidimensional scaling, and principal component analyses to identify general segregation patterns of trophic resources in relation to the habitat-use guild of bats and computed Pianka’s niche overlap index between species and Levin’s index to estimate the niche width of each species. Bats from the same locality tend to partition their diet, with a niche overlap ranging between 0.5 and 0.8. The highest values were found between species with different foraging behaviors. We suggest that future bat diet studies should incorporate the ecological and taxonomic information of arthropod prey to better understand the trophic interactions with bats.

We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9de novoassemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and non-invasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.

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.

The Amazonian marsh rat

Mazama temama (Kerr, 1792) is a representative species of the northern Neotropics, but the geographic range limits for this species remain unclear. We report the southernmost record of M. temama from the southwestern Colombian Andes, increasing the previously known range of this species by more than 300 km. We obtained a cytochrome gene sequence (849 bp) which is 95% identical to samples from Mexico. This record raises the need for extensive sampling to obtain more complete information about the distribution of M. temama in northern Colombia.

Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new associations between bat species and coronaviruses. However, RNA viruses are difficult to study in historical specimens because protocols for extracting RNA from these specimens have not been optimized. Advances have been made in our ability to recover nucleic acids from formalin-fixed paraffin-embedded samples (FFPE) commonly used in human clinical studies, yet other types of formalin preserved samples have received less attention. Here, we optimize the recovery of RNA from formalin-fixed ethanol-preserved museum specimens in order to improve the usability of these specimens in surveys for zoonotic diseases. We provide RNA quality and quantity measures for replicate tissues subsamples of 22 bat specimens from five bat genera (Rhinolophus, Hipposideros, Megareops, Cynopterus, and Nyctalus) collected in China and Myanmar from 1886 to 2003. As tissues from a single bat specimen were preserved in a variety of ways, including formalin-fixed (8 bats), ethanol-preserved and frozen (13 bats), and flash frozen (2 bats), we were able to compare RNA quality and yield across different preservation methods. RNA extracted from historical museum specimens is highly fragmented, but usable for short-read sequencing and targeted amplification. Incubation of formalin-fixed samples with Proteinase-K following thorough homogenization improves RNA yield. This optimized protocol extends the types of data that can be derived from existing museum specimens and facilitates future examinations of host and pathogen RNA from specimens.

The Mediterranean region is identified as one of the world’s 36 biodiversity hotspots, with the Earth’s most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.

The crested rat, Lophiomys imhausi, is the only mammal known to sequester plant toxins. Found in eastern Africa, this large rodent is thought to defend against predation by coating specialized hairs along its sides with cardenolide toxins from the poison arrow tree, Acokanthera schimperi. To better understand the ecology of this unusual poisonous mammal, we used camera traps, livetrapping, and captive behavioral observations, to study L. imhausi in central Kenya. Although crested rats were rarely detected with camera traps, 25 individuals were caught in live traps, with estimated densities of up to 15 rats/km2 at one of nine trapping sites. Trapping records and behavioral observations suggest that L. imhausi live in male–female pairs, with juveniles that might exhibit delayed dispersal. We observed chewing of A. schimperi and/or anointing in 10 of 22 individuals, confirming the previous poison sequestration observation. We monitored crested rat activity using cameras and found that chewing on A. schimperi and cardenolide exposure had no effect on feeding, movement, or total activity. One crested rat also fed on milkweed (Gomphocarpus physocarpus; Gentaniales: Apocynaceae), but did not anoint with this cardenolide containing plant. This observation, combined with L. imhausi’s selective use of A. schimperi, suggests the potential for use of alternative poison sources. This research provides novel insight into the ecology of L. imhausi, while also suggesting that more field observations, feeding trials, and chemical analyses are needed to understand their behavior and physiology. Furthermore, their complex social interactions, slow life history, and fragmented populations suggest that L. imhausi could be at risk of decline.

Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.

The marbled polecat, Vormela peregusna, is one of the least studied species in the Mustelidae family, especially with regard to phylogeography and genetic diversity. In this study, we determined th...

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 spe...

Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species *and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce SNP genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic single nucleotide polymorphism (SNP) loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats that we collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbors a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.

The Egyptian mongoose, Herpestes ichneumon, is the only extant mongoose in Europe, with populations still distributed in Africa and the Middle East. In this study, we present the first mitochondria...

Evolutionary radiations stemming from colonization of archipelagos provide valuable insights into mechanisms and modes of speciation. For this reason, the fauna inhabiting the Galapagos Islands has been the focus of numerous emblematic ecological and evolutionary studies. However, studies focused on rodents have been scarce. Rice rats radiated in situ into at least seven endemic species: Aegialomys galapagoensis, Nesoryzomys narboroughi, N. swarthi, N. fernandinae, N. indefessus, N. darwini and Megaoryzomys curioi. Only the first four species remain extant on the archipelago. These species are considered vulnerable, mainly due to human activities and invasive species. Despite their interesting evolutionary history, questions surrounding phylogenetic relationships, colonization events, genetic diversity and demography of populations remain unresolved. We used the D-loop region of mtDNA to infer phylogenetic relationships, colonization events, date divergences, and conduct population genetic analyses of the four extant endemic species inhabiting the Galapagos Islands. We found that all species were monophyletic. A. galapagoensis is sister to A. xanthaeolus from the continent, and both of them are the sister clade of the genus Nesoryzomys. Our results also showed that there were two colonization events to the islands. The first event was the arrival of the ancestor of Nesoryzomys during the Pliocene, when divergences between genera occurred. The second was Aegialomys during middle Pleistocene, when species diversification began. Populations on each island show high genetic diversity and most show signals of recent expansion. However, future studies are needed to accurately assess the conservation status of these populations. We suggest ongoing monitoring of these vulnerable endemic species, including ecological and population genetic studies. In addition, future studies using genome-wide molecular markers and additional species from the continent, as well as sampling extinct species from the islands, will improve our knowledge about the origin and relationships of the endemic rodents of the Galapagos Islands.

Age‐associated DNA‐methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human‐elephant clocks were constructed by combining human and elephant samples. Epigenome‐wide association studies identified elephant age‐related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, and targets of polycomb repressive complexes. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends., DNA methylation aging clocks for African and Asian elephants. Some of these clocks apply to humans as well. Parts of the graphic were created by Hollis Burbank‐Hammerlund, Sandra Oviedo, and BioRender.com.

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

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.

The marbled polecat, Vormela peregusna, is one of the least studied species in the Mustelidae family, especially with regard to phylogeography and genetic diversity. In this study, we determined the mitochondrial genome sequence of V. peregusna and investigated its position within the Mustelidae phylogeny. The generated mitogenome is 15,982 bp in length; it consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region.

The Egyptian mongoose, Herpestes ichneumon, is the only extant mongoose in Europe, with populations still distributed in Africa and the Middle East. In this study, we present the first mitochondrial genome sequence of Herpestes ichneumon and we investigate its phylogenetic position within Feliformia suborder. The resultant mitogenome sequence is 16,775 bps, composed of a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Our results represent a valuable resource for further phylogeographical studies.

Most of the Earth’s biodiversity is concentrated in the tropics. While the ultimate causes of this geographic pattern remain to be established, ongoing anthropogenic impacts in the tropical belt lead to rapid losses of species diversity. Ancient DNA approaches may help in deciphering temporal patterns in the diversification of tropical biota and could potentially provide historical baseline data on the diversity and distribution of species in anthropogenically modified landscapes. However, studies of sedimentary ancient DNA (sedaDNA) are thus far extremely rare in tropical settings and consequently its value as a conservation tool for tropical ecosystems remains to be tested systematically. To address this issue we present meta-genomic records of shot-gun sequenced sedimentary ancient DNA (sedaDNA) from several sediment cores from the equatorial Bwindi-Impenetrable Forest in Uganda. Because Bwindi is one the most diverse rainforests in Africa and its biota is well documented (including endangered species such Mountain Gorilla and Chimpanzee) it is well suited for a baseline study. We describe the taxonomic composition of sedaDNA from Bwindi for the past 2200 years at an average resolution of 50 years – one of the first comprehensive sedaDNA records of plant and animal taxa from a tropical rainforest. We specifically address the following questions: 1) How precisely can the taxonomic level of shotgun-sequenced tropical sediments be resolved at present? 2) What is the effect of temperature, acidity, nutrient availability, elemental and lithological sediment composition, and burial age on the degradation of DNA? Taxonomic assignments are based on three metagenomic classifiers and four reference databases and their reliability tested against local pollen and modern animal occurrence data. We find that 92.3% of our metagenomic data is taxonomically not identifiable due to the substantial underrepresentation of tropical taxa in genomic reference databases. Yet at ordinal level we reconstruct typical afrotropical assemblages, which do not decline in diversity over time. Our comprehensive set of ecological and sedimentological parameters including sediment age, surface water chemistry, pH, soil temperature, sediment density, sediment water and organic matter content, XRF elemental chemistry, nutrient concentrations, and magnetic susceptibility reveals that DNA degradation cannot be explained by any sedimentary parameter alone, is at Bwindi independent of sediment type, and most likely primarily driven by burial age, suggesting that DNA taphonomic models need to be site-specific in tropical environments. The viability of sedaDNA as a conservation-biology tool requires comprehensive genomic surveys of tropical biota to drastically improve the taxonomic representativeness of DNA reference databases.

Four species of spotted skunks (Carnivora, Mephitidae, Spilogale) are currently recognized: Spilogale angustifrons, S. gracilis, S. putorius, and S. pygmaea. Understanding species boundaries within this group is critical for effective conservation given that regional populations or subspecies (e.g., S. p. interrupta) have experienced significant population declines. Further, there may be currently unrecognized diversity within this genus as some taxa (e.g., S. angustifrons) and geographic regions (e.g., Central America) never have been assessed using DNA sequence data. We analyzed species limits and diversification patterns in spotted skunks using multilocus nuclear (ultraconserved elements) and mitochondrial (whole mitogenomes and single gene analysis) data sets from broad geographic sampling representing all currently recognized species and subspecies. We found a high degree of genetic divergence among Spilogale that reflects seven distinct species and eight unique mitochondrial lineages. Initial divergence between S. pygmaea and all other Spilogale occurred 29 in the Early Pliocene (~ 5.0 million years ago) which was followed by subsequent diversification of the remaining Spilogale into an “eastern” and “western” lineage during the Early Pleistocene (~1.5 million years ago). These two lineages experienced temporally coincident patterns of diversification at ~0.66 and ~0.35 million years ago into two and ultimately three distinct evolutionary units, respectively. Diversification was confined almost entirely within the Pleistocene during a timeframe characterized by alternating glacial-interglacial cycles, with the origin of this diversity occurring in northeastern Mexico and the southwestern United States of America. Mitochondrial-nuclear discordance was recovered across three lineages in geographic regions consistent with secondary contact, including a distinct mitochondrial lineage confined to the Sonoran Desert. Our results have direct consequences for conservation of threatened populations, or species, as well as for our understanding of the evolution of delayed implantation in this enigmatic group of small carnivores.

Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age (“epigenetic clocks”) in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human-elephant clocks were constructed by combing human and elephant samples. Epigenome-wide association studies identified elephant age-related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, targets of polycomb repressive complexes, and TFAP2C binding sites. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.

A surprising amount of hidden phylogenetic diversity exists in the small to medium size, drab colored squirrels of the genus Sundasciurus. This genus is endemic to Sundaland and the Philippines, where it is widespread. An earlier revision of this genus found that the high elevation ‘populations’ of the widespread, lowland slender squirrel (S. tenuis) were different species. Previous phylogenies based on mitochondrial cytochrome b sequences also suggested that the widespread, lowland Low’s squirrel (S. lowii) and the narrow endemic Fraternal squirrel (S. fraterculus) are not reciprocally monophyletic. Additionally, deep divergences have been identified between lineages within Low’s squirrel that date to the early Pliocene. Here we focus on evaluating the relationships and differences within and between populations of these two nominal species using whole mitochondrial genome sequences, nuclear intron sequences, and morphology. We reassess the taxonomy of this group, revalidate the species status of Robinson’s squirrel (Sundasciurus robinsoni Bonhote, 1903) support the species level recognition of the Natuna squirrel (Sundasciurus natunensis Thomas, 1895) and identify three other lineages that require further study. We estimate times of divergence and integrate geologic history to find that most of the divergences are pre-Pleistocene, and thus predate the Pleistocene flooding of Sundaland. Biogeographic, and ecological factors may have played a more important role than climatic factors in generating these patterns. While divergence in allopatry seems to be the main process driving speciation in lowland Sundaland squirrels (Sundasciurus), ecomorphological and behavioral adaptations in this clade suggest an important role of niche divergence., AH was supported by an Ernst Mayr Travel grant and AMNH Collection Study Grant during museum data collection. This research received support from the SYNTHESYS Project financed by European Community Research Infrastructure Action under the FP7 “Capacities” Program. AH was also supported by a Spanish Ministry of Economy contract CGL2014-58793-P. The Spanish Ministry of Science and Innovation grant CGL2017-86068-P to JL supported this study. MH was supported by discretionary research funding from Humboldt State University.

The endangered San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is strongly linked ecologically to xeric areas with high abundance of kangaroo rats. Endemic to the San Joaquin Desert of central California, the elusive nature of SJKF, coupled with steady habitat loss and lack of comprehensive surveys, has precluded efforts to quantify the species’ population size and distribution, especially in the central and northern parts of its range. Because the Ciervo-Panoche Natural Area contains the largest area of high-quality habitat in this central/northern region, we conducted systematic transect surveys for SJKF scats with professionally trained dog-handler teams throughout the area during 2009–2011. We collected almost 600 scats over 473 km of transects, documenting the freshness and location of each scat. Using molecular methods, we identified 93 SJKF individuals (56 males and 37 females) from 332 samples. Half of the individuals carried a mtDNA haplotype with a 16 bp deletion that had not been previously detected in other areas surveyed. Four individuals were recaptured in 2010 and five in 2011, including one female that was captured every year. We documented a unique mtDNA haplotype and more individuals across a wider area of the Ciervo-Panoche Natural Area than expected. Population analyses revealed two distinct subpopulations, with low connectivity between foxes in the Panoche Valley that are separated by hills with unsuitable habitat from those on the adjacent valley floor next to a major Interstate highway (I-5). While individuals detected within 6 km of each other were closely related, overall relatedness within each subpopulation approached zero. Genetic population models indicated a conservative population estimate of 90 kit foxes in total, with 60–90 individuals in the Panoche Valley and 17–27 individuals in the I-5 area. These results will help to inform management of the SJKF and identify areas that may be important to maintaining connectivity between populations.

The crested rat, Lophiomys imhausi, is the only mammal known to sequester plant toxins. Found in eastern Africa, this large rodent is thought to defend against predation by coating specialized hairs along its sides with cardenolide toxins from the poison arrow tree, Acokanthera schimperi. To better understand the ecology of this unusual poisonous mammal, we used camera traps, livetrapping, and captive behavioral observations, to study L. imhausi in central Kenya. Although crested rats were rarely detected with camera traps, 25 individuals were caught in live traps, with estimated densities of up to 15 rats/km(2) at one of nine trapping sites. Trapping records and behavioral observations suggest that L. imhausi live in male–female pairs, with juveniles that might exhibit delayed dispersal. We observed chewing of A. schimperi and/or anointing in 10 of 22 individuals, confirming the previous poison sequestration observation. We monitored crested rat activity using cameras and found that chewing on A. schimperi and cardenolide exposure had no effect on feeding, movement, or total activity. One crested rat also fed on milkweed (Gomphocarpus physocarpus; Gentaniales: Apocynaceae), but did not anoint with this cardenolide containing plant. This observation, combined with L. imhausi’s selective use of A. schimperi, suggests the potential for use of alternative poison sources. This research provides novel insight into the ecology of L. imhausi, while also suggesting that more field observations, feeding trials, and chemical analyses are needed to understand their behavior and physiology. Furthermore, their complex social interactions, slow life history, and fragmented populations suggest that L. imhausi could be at risk of decline.

Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.

Key insights into the evolutionary history of recently extinct or critically endangered species can be obtained through analysis of genomic data collected using high-throughput sequencing and ancient DNA from museum specimens, particularly where specimens are rare. For instance, the evolutionary history of the critically endangered Puebla deer mouse, Peromyscus mekisturus, remains unclear due to discordance between morphological and molecular phylogenetic analyses. However, previous molecular analyses were based on PCR and Sanger sequencing of only a few mitochondrial genes. Here, we used ancient DNA from historical museum specimens followed by target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and whole mitochondrial genomes to test the validity of the previous phylogenetic placement of P. mekisturus. Based on UCEs and mitogenomes, our results revealed that P. mekisturus forms a well-supported distinct lineage outside the clade containing all other members of the Peromyscus melanophrys group. Additionally, the mitogenome phylogeny further supports the placement of P. mekisturus as the sister species of the genus Reithrodontomys. This conflicts with the previous mtDNA phylogenetic reconstruction, in which P. mekisturus was nested within the species P. melanophrys. Our study demonstrates that high-throughput sequencing of ancient DNA, appropriately controlling for contamination and degradation, can provide a robust resolution of the evolutionary history and taxonomic status of species for which few or no modern genetic samples exist. In light of our results and pending further analysis with denser taxon sampling and the addition of morphological data, a re-evaluation of the taxonomy and conservation management plans of P. mekisturus is needed to ensure that the evolutionary distinctiveness of this species is recognized in future conservation efforts.

High-throughput sequencing methods have facilitated obtaining large amounts of data from degraded DNA, thus resulting in a dramatic increase in destructive sampling requests to museums. Because the tissues taken from museum specimens as sources of DNA are destroyed during analysis, consideration of the costs and benefits of loss of valuable specimen material relative to knowledge gained is required for any project utilizing destructive sampling. Variation exists in the preservation of DNA in historical specimens due to specimen age and type of museum preparation, among other factors. Thus, it is important to assess DNA yield and quality from different sources of museum specimens when considering the needs of a particular molecular project. We compared DNA derived from several common sources of museum specimens including bone, claw, skin, and soft tissue adherent to skeletal preparations. To account for differences in preparation type and therefore specimen preservation, we tested the performance of samples representing 3 taxonomic groups: mephitids, rodents, and marsupials. We also compared yields from 2 commonly used DNA extraction techniques. DNA quality was assessed by comparing average fragment size, concentration, and copy number of template DNA (for mitochondrial and nuclear markers) in genomic DNA extracts, as well as mitochondrial genome sequence coverage resulting from shotgun sequencing. We show that DNA quality derived from historic museum samples differs depending on specimen and sample type; however, all samples yielded high mitochondrial copy number except the skin and nail from the tanned specimen. Overall, claw samples produced the greatest number of high-quality sequencing reads with the least amount of bacterial contamination. We also found that high DNA concentrations did not necessarily result in high percentages of on-target reads; in fact, the samples that yielded the highest DNA quantities also had the highest amount of exogenous bacterial DNA. Our results indicate that most historical tissue types can be suitable for next-generation sequencing approaches, therefore providing multiple options for natural history collection staff and researchers when considering destructive sampling requests.

Made available in DSpace on 2018-11-26T17:44:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-01-01 Programa de Desarrollo de las Ciencias Basicas (PEDECIBA, Uruguay) Agencia Nacional de Investigacion e Innovacion (ANII, Uruguay) Smithsonian Conservation Biology Institute Center for Conservation Genomics (Washington, DC, USA) Smithsonian Institution National Geographic Society Wildlife Conservation Society The maned wolf Chrysocyon brachyurus is the largest South American canid and categorized as Near Threatened on the IUCN Red List. The major threat to conservation efforts is the drastic reduction of suitable habitat for the species. A large portion of its range has been converted into farm and ranch lands as well as urban areas. To better understand the impact that these anthropogenic activities are having over the remaining populations across their current distribution range, we evaluated patterns of genetic variability and differentiation between them. We also compared these results with those obtained from captive maned wolves in order to make proper ex situ recommendations. We cross-amplified 12 microsatellite loci in maned wolf samples collected throughout their range (from Argentina, Brazil, Uruguay and Bolivia) and from captive stocks (from captive breeding centers and zoos in Brazil, Argentina and the USA). We found that wild populations retain moderate levels of genetic variability compared with other microsatellite studies on wild canids, and our structure analysis revealed 2 genetic clusters in wild samples, one of which included samples exclusively from Bolivia. This cluster could represent a different management unit with conservation priority. The captive stock population showed higher levels of genetic variability, with the ones from Brazil being the most genetically diverse stock. The USA stock showed strong genetic differences with all other groups. This is the first study to examine the patterns of genetic diversity of both wild and captive populations of maned wolves. These results should be incorporated into further population viability assessments and in the Maned Wolf Species Survival Plan. IIBCE, Dept Biodiversidad & Genet, Genet Conservac, Montevideo 11600, Uruguay Univ Republ UdelaR, Fac Ciencias, Secc Genet Evolut, Montevideo 11400, Uruguay Smithsonian Inst, Natl Museum Nat Hist, Dept Vertebrate Zool, Washington, DC 20013 USA Univ Estadual Paulista, Dept Zootecnia, Nucleo Pesquisa & Conservacao Cervideos, BR-14884900 Jaboticabal, SP, Brazil Minist Ambiente & Desarrollo Sustentable, RA-1004 Buenos Aires, DF, Argentina Smithsonian Conservat Biol Inst, Natl Zool Pk, Ctr Conservat Gen, Washington, DC 20008 USA Univ Estadual Paulista, Dept Zootecnia, Nucleo Pesquisa & Conservacao Cervideos, BR-14884900 Jaboticabal, SP, Brazil Agencia Nacional de Investigacion e Innovacion (ANII, Uruguay): FCE_3_2011_1_6619

The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation.

Genes of the major histocompatibility complex (MHC) play a primary role in resistance to infectious disease and have been implicated in mate choice and recognition of close relatives. We describe genetic diversity at three MHC class II genes in urban and non-urban populations of San Joaquin kit fox (Vulpes macrotis mutica), an endangered canid endemic to California’s San Joaquin Valley. We used multi-tagged pyrosequencing synthesis to characterize genetic diversity in 96 kit foxes at three MHC class II genes, DQA1, DQB1, and DRB1. Using rigorous bioinformatics methods to limit sequencing artifacts, we identified 11 DQA alleles, 13 DQB alleles, and 29 DRB alleles, which translated into 1, 7, and 28 unique antigen-binding sites for the respective genes. The high polymorphism did not correlate with sequencing depth or sample location but was found across individuals and indicated polygenic loci for DQB (two gene copies) and DRB (three copies). A phylogeny based on all known carnivore MHC alleles resolved two major clades, one with alleles from DQA and one with alleles from DQB and DRB, regardless of the taxa. Based on Tajima’s D, we found evidence of negative selection in DQA (D = −1.90) and positive selection in DRB (D = 2.36). We analyzed 48 urban kit foxes that were living in the city of Bakersfield and 48 non-urban foxes living in the nearby LoKern and Carrizo plain areas. We found similar levels of MHC allelic diversity in the urban and non-urban populations. However, many of the common DRB alleles found in the non-urban population were absent in the urban population. This could result from a founder effect or different selective pressures on the two populations. The levels of MHC diversity in the SJKF are similar to or higher than MHC diversity of more wide-spread canid species, although this subspecies has been isolated in the San Joaquin Valley for millennia and has low mtDNA haplotype diversity. Our study provides baseline data on three MHC genes that can contribute to future studies of disease resistance and mate choice in the endangered San Joaquin kit fox.

Population monitoring is critical to effective conservation, but forest living taxa can be difficult to directly observe. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas in southwestern Gabon, which is considered a global stronghold for forest elephants. Additionally, we examined social networks, predicting that we would find matrilineal structure seen in both savanna and forest elephants. Given 95% confidence intervals, we estimate population size in the sampled area to be between 754 and 1,502 individuals and our best density estimate ranges from 0.47 to 0.80 elephants per km2. When extrapolated across the entire Industrial Corridor, this estimate suggests an elephant population size of 3,033 to 6,043 based on abundance or 1,684 to 2,832 based on density, approximately 40–80% smaller than previously suggested. Our social network analysis revealed approximately half of network components included females with different mitochondrial haplotypes suggesting a wider range of variation in forest elephant sociality than previously thought. This study emphasizes the threatened status of forest elephants and demonstrates the need to further refine baseline estimates of population size and knowledge on social behavior in this taxon, both of which will aid in determining how population dynamics in this keystone species may be changing through time in relation to increasing conservation threats.

Karuppannan KV, Aifat NR, Mohamed KA, Ahmad-Tahir NFD, Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.

Coatis (Procyonidae; Nasua) are considered the only truly social meso-carnivore mammals in Neotropical forests. In Mexico, white-nosed coatis (Nasua narica) are suspected to have undergone population reduction due to habitat loss and fragmentation and led to a lack of genetic adaptability and genetic isolation throughout its range. We examined patterns of genetic diversity and connectivity of five populations of Nasua narica distributed throughout Mexico (n = 60) by sequencing an ≈ 800 bp fragment of the mitochondrial cytochrome-b gene and also by screening 12 microsatellite loci. We found moderate to high levels of genetic variability for both genetic markers. We recorded twenty-two different cytochrome-b haplotypes throughout the 5 sampled areas and found that each of the sampled population of white-nosed coatis in Mexico harbors unique haplotypes and only three haplotypes were shared among two different populations that were closer geographically. All populations had high haplotype diversity (h) (0.968 ± 0.008 (SD)) but lower levels of nucleotide diversity (π) of 0.007 ± 0.001 (SD). All microsatellite loci were polymorphic in all of the populations and the mean number of alleles per locus was 5.033 ± 1.545 (SD) with expected (HE) and observed (HO) heterozygosity values of 0.774 and 0.664, respectively. However, low Wright F statistic values suggest the existence of a reduced heterozygosity (FST = 0.203, FIS = 0.134 and FIT = 0.310). Significant differences between the five populations confirmed isolation by distance, which suggests genetic structure among five subpopulations.

Understanding how human activities have influenced the foraging ecology of wildlife is important as our planet faces ongoing and impending habitat and climatic change. We review the canine surrogacy approach (CSA)—a tool for comparing human, dog, and other canid diets in the past—and apply CSA to investigate possible ancient human resource provisioning in an endangered canid, the California Channel Islands fox (Urocyon littoralis). We conducted stable isotope analysis of bone collagen samples from ancient and modern island foxes (n = 214) and mainland gray foxes (Urocyon cinereoargenteus, n = 24). We compare these data to isotope values of ancient humans and dogs, and synthesize 29 Accelerator Mass Spectrometry (AMS) radiocarbon dates that fine-tune the chronology of island foxes. AMS dates confirm that island foxes likely arrived during the early Holocene (>7300 cal BP) on the northern islands in the archipelago and during the middle Holocene (>5500 cal BP) on the southern islands. We found no evidence that island foxes were consistently using anthropogenic resources (e.g., food obtained by scavenging around human habitation sites or direct provisioning by Native Americans), except for a few individuals on San Nicolas Island and possibly on San Clemente and Santa Rosa islands. Decreases in U. littoralis carbon and nitrogen isotope values between prehistoric times and the 19th century on San Nicolas Island suggest that changes in human land use from Native American hunter-gatherer occupations to historical ranching had a strong influence on fox diet. Island foxes exhibit considerable dietary variation through time and between islands and have adapted to a wide variety of climatic and cultural changes over the last 7300 years. This generalist foraging strategy suggests that endemic island foxes may be resilient to future changes in resource availability.

Ectoparasites frequently vector pathogens from often unknown pathogen reservoirs to both human and animal populations. Simultaneous identification of the ectoparasite species, the wildlife host that provided their most recent blood meal(s), and their pathogen load would greatly facilitate the understanding of the complex transmission dynamics of vector-borne diseases. Currently, these identifications are principally performed using multiple polymerase chain reaction (PCR) assays. We developed an assay (EctoBaits) based on in-solution capture paired with high-throughput sequencing to simultaneously identify ectoparasites, host blood meals and pathogens. We validated our in-solution capture results using double-blind PCR assays, morphology and collection data. The EctoBaits assay effectively and efficiently identifies ectoparasites, blood meals, and pathogens in a single capture experiment, allowing for high-resolution taxonomic identification while preserving the DNA sample for future analyses.

Sex determination among wild Asian elephant (Elephas maximus) populations in Taman Negara National Parks (TNPP), Peninsular Malaysia were very crucial by using ecological techniques such as biodiversity inventories or dung count survey. With advance molecular sexing technique, the sex ratio among wild E. maximus in study area can be determined. As a first move, we conduct this particular experiment by using two Y-specific and one X-specific molecular sexing primers on 63 wild Asian elephant faecal samples together with 10 positive controls from known elephant individuals in National Elephant Conservation Centre (NECC) Kuala Gandah, Pahang, Peninsular Malaysia. DNA extraction were done by using Qiagen kits and we carried out multiplex PCR and visualized those PCR products on agarose gel before proceed with fragment analysis. Fragment analyses with 3 peaks were confirmed for male while female showed the expected 1 peak. The outcome showed, 31 samples were from female elephants while remaining 32 samples from male. This is very significant and strong outcome which proofs that molecular sexing markers can be used in non-invasive samples as well and be a good baseline data to study Asian elephant social organization in TNPP, Peninsular Malaysia.

Myotis planiceps (flat-headed myotis) was known from only 3 specimens collected from 3 different sites in the states of Coahuila, Nuevo Leon, and Zacatecas, Mexico, since its discovery in 1952. The last specimen was collected in 1970; in 1996, after efforts to recollect samples failed, the species was listed as extinct. However, an expedition in 2004 rediscovered a population of M. planiceps and the species was relisted as endangered. Members of this species have a conspicuously flattened cranium, speculated to be an adaptation for living in crevices; however, little is known about its biology and, to date, little work has been done to clarify its phylogenetic relationships with other members of the genus Myotis . In order to elucidate the placement of M. planiceps within the Myotis phylogeny, we sequenced 1,140 base pairs (bps) of the mitochondrial cytochrome- b gene ( Cytb ) and 1,148 bps of the nuclear Recombination Activating Gene 2 ( rag2 ) from 7 samples collected from 4 different localities in north-central Mexico. We found 4 different haplotypes for Cytb that differed by 0.14% mean sequence divergence and 13 alleles for rag2 within samples of M. planiceps . We performed maximum parsimony, maximum likelihood, and Bayesian analyses to compare these samples with Myotis sequences available on GenBank. All reconstructions placed M. planiceps within a strongly supported clade including several Nearctic Myotis ( M. volans , M. sodalis , M. lucifugus , M. thysanodes , and M. evotis ). M. planiceps forms a paraphyletic relationship with M. volans , despite significant differences in skull morphology between the 2 species. Myotis planiceps (Myotis de cabeza plana) era conocido a partir de solo 3 especimenes recolectados en 3 sitios diferentes en los estados de Coahuila, Nuevo Leon y Zacatecas, Mexico, desde su descubrimiento en 1952. El ultimo ejemplar se colecto en 1970 y la especie fue declarada extinta en 1996, despues de que fallaron los esfuerzos para recolectar mas muestras. Sin embargo, durante una expedicion en 2004 se redescubrio una poblacion de M. planiceps y la especie fue recategorizada bajo Peligro de Extincion. Los miembros de esta especie tienen un craneo visiblemente aplanado, rasgo que se especula seria una adaptacion para vivir en las grietas; sin embargo, se sabe poco sobre su biologia y, hasta la fecha, poco se ha hecho para aclarar sus relaciones filogeneticas con otros miembros del genero Myotis . Con el fin de dilucidar la posicion de M. planiceps dentro de la filogenia de Myotis , secuenciamos 1140 pb del gen mitocondrial citocromo-b ( Cytb ) y 1148 pb del gen nuclear Activador de la Recombinacion 2 ( rag2 ) a partir de 7 muestras recolectadas de 4 localidades diferentes en la region norte-central de Mexico. Encontramos 4 haplotipos diferentes para Cytb que presentaron un promedio de divergencia de secuencia de 0.14%, y 13 alelos del gen rag2 en muestras de M. planiceps . Realizamos analisis de maxima parsimonia, maxima verosimilitud y Bayesiano para comparar estas muestras con otras secuencias de Myotis disponibles en GenBank. Todas las reconstrucciones ubican a M. planiceps dentro de un clado bien soportado que incluye tambien a varios Myotis del Neartico ( M. volans , M. sodalis , M. lucifugus , M. thysanodes , y M. evotis ). M. planiceps forma una relacion parafiletica con M. volans , a pesar de diferencias significativas en la morfologia del craneo entre estas especies.