Publications by authors named "Jesús E Maldonado"

56 Publications

Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification.

Mol Phylogenet Evol 2021 Jul 21:107266. Epub 2021 Jul 21.

Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park PO Box 37012 MRC 5503 Washington, DC 20013.

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 in the Early Pliocene (∼ 5.0 million years ago). Subsequent diversification of the remaining Spilogale into an "eastern" and a "western" lineage occurred 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.
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http://dx.doi.org/10.1016/j.ympev.2021.107266DOI Listing
July 2021

Epigenetic clock and methylation studies in elephants.

Aging Cell 2021 Jul 12;20(7):e13414. Epub 2021 Jun 12.

Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA.

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.
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http://dx.doi.org/10.1111/acel.13414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8282242PMC
July 2021

First mitochondrial genome of the marbled polecat (Carnivora, Mustelidae).

Mitochondrial DNA B Resour 2021 Mar 18;6(3):1009-1011. Epub 2021 Mar 18.

Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Beirut, Lebanon.

The marbled polecat, , 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 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.
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http://dx.doi.org/10.1080/23802359.2021.1894997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7995864PMC
March 2021

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

Mitochondrial DNA B Resour 2021 Mar 15;6(3):883-885. Epub 2021 Mar 15.

Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Beirut, Lebanon.

The Caucasian Squirrel, , is the only representative of the Sciuridae family in the Eastern Mediterranean region. In this study, the mitochondrial genome of the 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.
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http://dx.doi.org/10.1080/23802359.2021.1886012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971277PMC
March 2021

First mitochondrial genome of the Egyptian mongoose (Carnivora, Herpestidae).

Mitochondrial DNA B Resour 2021 Feb 19;6(2):624-626. Epub 2021 Feb 19.

Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Beirut, Lebanon.

The Egyptian mongoose, , 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 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.
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http://dx.doi.org/10.1080/23802359.2021.1875927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899645PMC
February 2021

Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats.

Ecol Evol 2021 Feb 19;11(4):1814-1828. Epub 2021 Jan 19.

Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA.

Rapid advances in genomic tools for use in ecological contexts and non-model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high-throughput sequencing on chicken () tissues collected over an 11-day decomposition study in natural Hawaiian habitats. Second, we determined if field-collected invasive black rats (;  = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high-throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds ( = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats ( = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird () and three introduced bird species (, , ) were detected in the rats' diets, with individuals from these species (except ) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.
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http://dx.doi.org/10.1002/ece3.7171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882976PMC
February 2021

The secret social lives of African crested rats, .

J Mammal 2020 Dec 17;101(6):1680-1691. Epub 2020 Nov 17.

School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.

The crested rat, , 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, To better understand the ecology of this unusual poisonous mammal, we used camera traps, livetrapping, and captive behavioral observations, to study 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 at one of nine trapping sites. Trapping records and behavioral observations suggest that live in male-female pairs, with juveniles that might exhibit delayed dispersal. We observed chewing of 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 and cardenolide exposure had no effect on feeding, movement, or total activity. One crested rat also fed on milkweed (; Gentaniales: Apocynaceae), but did not anoint with this cardenolide containing plant. This observation, combined with 's selective use of , suggests the potential for use of alternative poison sources. This research provides novel insight into the ecology of , 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 could be at risk of decline.
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http://dx.doi.org/10.1093/jmammal/gyaa127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816685PMC
December 2020

Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor).

Genome Biol Evol 2021 01;13(1)

Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.

Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection.
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http://dx.doi.org/10.1093/gbe/evaa255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851585PMC
January 2021

First DNA sequence reference library for mammals and plants of the Eastern Mediterranean Region.

Genome 2021 Jan 1;64(1):39-49. Epub 2020 Oct 1.

Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon.

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 rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the and 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.
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http://dx.doi.org/10.1139/gen-2019-0194DOI Listing
January 2021

Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient.

Mol Ecol 2020 11 28;29(21):4074-4090. Epub 2020 Sep 28.

Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.

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.
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http://dx.doi.org/10.1111/mec.15626DOI Listing
November 2020

Comparison of genomic diversity and structure of sable antelope () in zoos, conservation centers, and private ranches in North America.

Evol Appl 2020 Sep 27;13(8):2143-2154. Epub 2020 Apr 27.

Center for Species Survival, Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA.

As we enter the sixth mass extinction, many species that are no longer self-sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for holistic conservation programs between the public and private sector. Ex situ populations of sable antelope, , have existed in zoos and privately owned ranches in North America since the 1910s. Unknown founder representation and relatedness has made the genetic management of this species challenging within zoos, while populations on privately owned ranches are managed independently and retain minimal-to-no pedigree history. Consequences of such challenges include an increased risk of inbreeding and a loss of genetic diversity. Here, we developed and applied a customized targeted sequence capture panel based on 5,000 genomewide single-nucleotide polymorphisms to investigate the genomic diversity present in these uniquely managed populations. We genotyped 111 sable antelope: 23 from zoos, 43 from a single conservation center, and 45 from ranches. We found significantly higher genetic diversity and significantly lower inbreeding in herds housed in zoos and conservation centers, when compared to those in privately owned ranches, likely due to genetic-based breeding recommendations implemented in the former populations. Genetic clustering was strong among all three populations, possibly as a result of genetic drift. We propose that the North American ex situ population of sable antelope would benefit from a metapopulation management system, to halt genetic drift, reduce the occurrence of inbreeding, and enable sustainable population sizes to be managed ex situ.
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http://dx.doi.org/10.1111/eva.12976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463370PMC
September 2020

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

BMC Evol Biol 2020 06 26;20(1):77. Epub 2020 Jun 26.

Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA.

Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa.

Results: We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses-performed with datasets differing on levels of missing data and taxa under distinct analytical methods-strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels.

Conclusions: Complete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.
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http://dx.doi.org/10.1186/s12862-020-01639-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320592PMC
June 2020

Abundance, density, and social structure of African forest elephants (Loxodonta cyclotis) in a human-modified landscape in southwestern Gabon.

PLoS One 2020 29;15(4):e0231832. Epub 2020 Apr 29.

Department of Anthropology, University of Oregon, Eugene, OR, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231832PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190099PMC
July 2020

Endemism and diversity of small mammals along two neighboring Bornean mountains.

PeerJ 2019 8;7:e7858. Epub 2019 Oct 8.

Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Sevilla, Spain.

Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.
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http://dx.doi.org/10.7717/peerj.7858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788440PMC
October 2019

Concurrent visual encounter sampling validates eDNA selectivity and sensitivity for the endangered wood turtle (Glyptemys insculpta).

PLoS One 2019 24;14(4):e0215586. Epub 2019 Apr 24.

Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, United States of America.

Environmental DNA (eDNA) has been used to record the presence of many different organisms in several different aquatic and terrestrial environments. Although eDNA has been demonstrated as a useful tool for the detection of invasive and/or cryptic and declining species, this approach is subject to the same considerations that limit the interpretation of results from traditional survey techniques (e.g. imperfect detection). The wood turtle is a cryptic semi-aquatic species that is declining across its range and, like so many chelonian species, is in-need of a rapid and effective method for monitoring distribution and abundance. To meet this need, we used an eDNA approach to sample for wood turtle presence in northern Virginia streams. At the same time, we used repeat visual encounter surveys in an occupancy-modelling framework to validate our eDNA results and reveal the relationship of detection and occupancy for both methods. We sampled 37 stream reaches of varying size within and beyond the known distribution of the wood turtle across northern Virginia. Wood turtle occupancy probability was 0.54 (0.31, 0.76) and while detection probability for wood turtle occupancy was high (0.88; 0.58, 0.98), our detection of turtle abundance was markedly lower (0.28; 0.21, 0.37). We detected eDNA at 76% of sites confirmed occupied by VES and at an additional three sites where turtles were not detected but were known to occur. Environmental DNA occupancy probability was 0.55 (0.29, 0.78); directly comparable to the VES occupancy estimate. Higher probabilities of detecting wood turtle eDNA were associated with higher turtle densities, an increasing number of days since the last rainfall, lower water temperatures, and lower relative discharges. Our results suggest that eDNA technology holds promise for sampling aquatic chelonians in some systems, even when discharge is high and biomass is relatively low, when the approach is validated and sampling error is quantified.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215586PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481842PMC
January 2020

Whole Genome Sequencing and Re-sequencing of the Sable Antelope (): A Resource for Monitoring Diversity in and Populations.

G3 (Bethesda) 2019 06 5;9(6):1785-1793. Epub 2019 Jun 5.

Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, 22630 and Washington, DC 20008.

Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive () and wild () populations of threatened species. The sable antelope (), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.596 Gb draft genome consists of 136,528 contigs with an N50 of 45.5 Kbp and 16,927 scaffolds with an N50 of 4.59 Mbp. annotation identified 18,828 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species.
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http://dx.doi.org/10.1534/g3.119.400084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553546PMC
June 2019

High genetic diversity and distinct ancient lineage of Asiatic black bears revealed by non-invasive surveys in the Annapurna Conservation Area, Nepal.

PLoS One 2018 5;13(12):e0207662. Epub 2018 Dec 5.

Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan.

Asiatic black bears (Ursus thibetanus) have a widespread distribution in mountain landscapes, and are considered vulnerable globally, but are low-priority species for conservation in Nepal. Habitat fragmentation, illegal hunting, and human-bear conflict are the major threats to Asiatic black bears across their global range. Having an adequate level of genetic variation in a population helps with adapting to rapidly changing environments, and thus is important for the long-term health of bear populations. Accordingly, we conducted non-invasive surveys of bear populations in the Annapurna Conservation Area (ACA) to elucidate genetic diversity, genetic structure, and the phylogenetic relationship of Asiatic black bears from this region of Nepal to other subspecies. To assess levels of genetic diversity and population genetic structure, we genotyped eight microsatellite loci using 147 samples, identifying 60 individuals in an area of approximately 525 km2. We found that the Asiatic black bear population in the ACA has maintained high levels of genetic diversity (HE = 0.76) as compared to other bear populations from range countries. We did not detect a signature of population substructure among sampling localities and this suggests that animals are moving freely across the landscape within the ACA. We also detected a moderate population size that may increase with the availability of suitable habitat in the ACA, so bear-related conflict should be addressed to ensure the long-term viability of this expanding bear populations. Primers specific to bears were designed to amplify a 675 bp fragment of the mitochondrial control region from the collected samples. Three haplotypes were observed from the entire conservation area. The complete mitochondrial genome (16,771 bp), the first obtained from wild populations of the Himalayan black bear (U. t. laniger), was also sequenced to resolve the phylogenetic relationships of closely related subspecies of Asiatic black bears. The resulting phylogeny indicated that Himalayan black bear populations in Nepal are evolutionary distinct from other known subspecies of Asiatic black bears.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207662PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281213PMC
May 2019

A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling.

Zookeys 2017 14(697):87-131. Epub 2017 Sep 14.

Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, Washington DC, USA.

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of , , , , , , and . contains species that belong to other genera. We found a novel sister-taxon relationship between "" and a clade formed by and , and transfer to . The clade formed by and may represent a valid species, whereas the remaining subspecies of appear closer to . () was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic as a distinct genus. We provide evidence for the existence of an undescribed species now confused with , and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as , "" , and . Noteworthy records that substantially extend the known distributions of and "" are provided, and we unveil a surprising ambiguity regarding the distribution of "" , as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.
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http://dx.doi.org/10.3897/zookeys.697.15124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673856PMC
September 2017

Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus).

BMC Genomics 2016 12 9;17(1):1013. Epub 2016 Dec 9.

Center for Conservation Genomics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA.

Background: The African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage.

Results: We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection.

Conclusions: We show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage.
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http://dx.doi.org/10.1186/s12864-016-3368-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148847PMC
December 2016

Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska.

Conserv Biol 2017 10 15;31(5):1163-1172. Epub 2017 May 15.

Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A.

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.
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http://dx.doi.org/10.1111/cobi.12865DOI Listing
October 2017

Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens.

BMC Evol Biol 2016 Apr 14;16:80. Epub 2016 Apr 14.

Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.

Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea-an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships.

Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data.

Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7-12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.
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http://dx.doi.org/10.1186/s12862-016-0650-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831120PMC
April 2016

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

Mol Ecol 2016 May 5;25(10):2176-94. Epub 2016 Apr 5.

Department of Fish, Wildlife and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO, 80523, USA.

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
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http://dx.doi.org/10.1111/mec.13605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877267PMC
May 2016

Simultaneous identification of host, ectoparasite and pathogen DNA via in-solution capture.

Mol Ecol Resour 2016 Sep 4;16(5):1224-39. Epub 2016 Apr 4.

Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, DC, 20008, USA.

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.
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http://dx.doi.org/10.1111/1755-0998.12524DOI Listing
September 2016

Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae).

Mol Phylogenet Evol 2016 Jan 31;94(Pt B):752-764. Epub 2015 Oct 31.

Estación Biológica de Doñana (EBD-CSIC), Conservation and Evolutionary Genetics Group, Avda. Americo Vespucio s/n, Sevilla 41092, Spain.

The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine the tree topology, and date the tree. All speciation events within the plain-long nosed squirrels (genus Dremomys) were ancient (dated to the Pliocene or Miocene), and averaged older than many speciation events in the related Sunda squirrels, genus Sundasciurus. Within the plain long-nosed squirrels, the most recent interspecific split occurred 2.9 million years ago, older than some splits within Sunda squirrels, which dated to the Pleistocene. Our results demonstrate that the plain long-nosed squirrels are not monophyletic. The single species with a distinct distribution, the Bornean mountain ground squirrel (Dremomys everetti), which is endemic to the high mountains of Borneo, is nested within the Sunda squirrels with high support. This species diverged from its sister taxa in the Sunda squirrels 6.62 million years ago, and other plain long-nosed squirrels over 11 million years ago. Our analyses of morphological traits in these related genera support the re-classification of the Bornean mountain ground squirrel, Dremomys everetti, to the genus Sundasciurus, which changes its name to Sundasciurus everetti. Past inclusion in the plain long-nosed squirrels (Dremomys) reflects convergent evolution between these high elevation species.
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http://dx.doi.org/10.1016/j.ympev.2015.10.023DOI Listing
January 2016

Molecular Phylogeny Supports Repeated Adaptation to Burrowing within Small-Eared Shrews Genus of Cryptotis (Eulipotyphla, Soricidae).

PLoS One 2015 21;10(10):e0140280. Epub 2015 Oct 21.

Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America; Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C., United States of America.

Small-eared shrews of the New World genus Cryptotis (Eulipotyphla, Soricidae) comprise at least 42 species that traditionally have been partitioned among four or more species groups based on morphological characters. The Cryptotis mexicana species group is of particular interest, because its member species inhibit a subtly graded series of forelimb adaptations that appear to correspond to locomotory behaviors that range from more ambulatory to more fossorial. Unfortunately, the evolutionary relationships both among species in the C. mexicana group and among the species groups remain unclear. To better understand the phylogeny of this group of shrews, we sequenced two mitochondrial and two nuclear genes. To help interpret the pattern and direction of morphological changes, we also generated a matrix of morphological characters focused on the evolutionarily plastic humerus. We found significant discordant between the resulting molecular and morphological trees, suggesting considerable convergence in the evolution of the humerus. Our results indicate that adaptations for increased burrowing ability evolved repeatedly within the genus Cryptotis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140280PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619083PMC
June 2016

Phylogeography of the Golden Jackal (Canis aureus) in India.

PLoS One 2015 28;10(9):e0138497. Epub 2015 Sep 28.

Wildlife Institute of India, Chandrabani, Dehradun 248001, India.

The golden jackal (Canis aureus) is one of the most common and widely distributed carnivores in India but phylogeographic studies on the species have been limited across its range. Recent studies have observed absence of mitochondrial (mt) DNA diversity in European populations while some North African populations of golden jackal were found to carry gray wolf (Canis lupus lupaster) mtDNA lineages. In the present study, we sequenced 440 basepairs (bp) of control region (CR) and 412 bp of cytochrome b (cyt b) gene of mtDNA from 62 golden jackals sampled from India (n = 55), Israel (n = 2) and Bulgaria (n = 5), to obtain a total of eighteen haplotypes, comprising sixteen from India and one each from Israel and Bulgaria. Except for three previously described haplotypes represented by one cyt b and one CR haplotype both from India, and one CR haplotype from Bulgaria, all haplotypes identified in this study are new. Genetic diversity was high in golden jackals compared to that reported for other canids in India. Unlike the paraphyletic status of African conspecifics with the gray wolf, the Indian (and other Eurasian) golden jackal clustered in a distinct but shallow monophyletic clade, displaying no evidence of admixture with sympatric and related gray wolf and domestic dog clades in the region. Phylogeographic analyses indicated no clear pattern of genetic structuring of the golden jackal haplotypes and the median joining network revealed a star-shaped polytomy indicative of recent expansion of the species from India. Indian haplotypes were observed to be interior and thus ancestral compared to haplotypes from Europe and Israel, which were peripheral and hence more derived. Molecular tests for demographic expansion confirmed a recent event of expansion of golden jackals in the Indian subcontinent, which can be traced back ~ 37,000 years ago during the late Pleistocene. Our results suggest that golden jackals have had a potentially longer evolutionary history in India than in other parts of the world, although further sampling from Africa, the Middle East and south-east Asia is needed to test this hypothesis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138497PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586146PMC
June 2016

Population Structure of mtDNA Variation due to Pleistocene Fluctuations in the South American Maned Wolf (Chrysocyon brachyurus, Illiger, 1815): Management Units for Conservation.

J Hered 2015 ;106 Suppl 1:459-68

From the Genética de la Conservación-Departamento de Biodiversidad y Genética -IIBCE- MEC Av. Italia 3318 Montevideo 11600, Uruguay (González, Cosse, and del Rosario Franco); Sección Genética Evolutiva Facultad de Ciencias UdelaR, Montevideo 11600, Uruguay (González); Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, NHB W630, MRC108, P.O. Box 37012, Washington, DC 20013-7012 (Emmons and Maldonado); Science and evaluation, National Fish and Wildlife Foundation, 1133 Fifteenth St., N.W., Suite 1100 Washington, DC 20005 (Vynne); Núcleo de Pesquisa e Conservação de Cervídeos, Departamento de Zootecnia / Universidade Estadual Paulista Via de Acesso Paulo Donato Castellane, s/n 14884-900 Jaboticabal - SP-Brasil (Duarte); Secretaría de Ambiente y Desarrollo Sustentable de la Nación, Reconquista 555, Buenos Aires, Argentina (Beccacesi); and Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Ave. NW, Washington DC 20008 (Maldonado).

The maned wolf (Chrysocyon brachyurus) is one of the largest South American canids, and conservation across this charismatic carnivore's large range is presently hampered by a lack of knowledge about possible natural subdivisions which could influence the population's viability. To elucidate the phylogeographic patterns and demographic history of the species, we used 2 mtDNA markers (D-loop and cytochrome b) from 87 individuals collected throughout their range, in Argentina, Bolivia, Brazil, and Uruguay. We found moderate levels of haplotype and nucleotide diversity, and the 14 D-loop haplotypes were closely related. Genetic structure results revealed 4 groups, and when coupled with model inferences from a coalescent analysis, suggested that maned wolves have undergone demographic fluctuations due to changes in climate and habitat during the Pleistocene glaciation period approximately 24000 years before present (YBP). This genetic signature points to an event that occurred within the timing estimated for the start of the contraction of the Cerrado around 50000 YBP. Our results reveal a genetic signature of population size expansion followed by contraction during Pleistocene interglaciations, which had similar impacts on other South American mammals. The 4 groups should for now be considered management units, within which future monitoring efforts should be conducted independently.
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http://dx.doi.org/10.1093/jhered/esv043DOI Listing
October 2015

In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA.

Mol Ecol Resour 2016 Sep 24;16(5):1173-88. Epub 2015 Aug 24.

Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules.
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http://dx.doi.org/10.1111/1755-0998.12448DOI Listing
September 2016

Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene.

Trends Ecol Evol 2015 Sep 11;30(9):540-9. Epub 2015 Jul 11.

Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20013-7012, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.

There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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http://dx.doi.org/10.1016/j.tree.2015.06.008DOI Listing
September 2015

The Taxonomic Status of Mazama bricenii and the Significance of the Táchira Depression for Mammalian Endemism in the Cordillera de Mérida, Venezuela.

PLoS One 2015 29;10(6):e0129113. Epub 2015 Jun 29.

Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America.

We studied the taxonomy and biogeography of Mazama bricenii, a brocket deer classified as Vulnerable by the IUCN, drawing on qualitative and quantitative morphology and sequences of the mitochondrial cytochrome-b gene. We used Ecological Niche Modeling (ENM) to evaluate the hypothesis that M. bricenii of the Venezuelan Cordillera de Mérida (CM) might have become isolated from populations of its putative sister species, Mazama rufina, in the Colombian Cordillera Oriental (CO). This hypothesis assumes that warm, dry climatic conditions in the Táchira Depression were unsuitable for the species. Our analyses did not reveal morphological differences between specimens geographically attributable to M. bricenii and M. rufina, and phylogenetic analyses of molecular data recovered M. bricenii nested within the diversity of M. rufina. These results indicate that M. bricenii should be regarded as a junior synonym of M. rufina. ENM analyses revealed the existence of suitable climatic conditions for M. rufina in the Táchira Depression during the last glacial maximum and even at present, suggesting that gene flow between populations in the CO and CM may have occurred until at least the beginning of the current interglacial period and may continue today. Because this pattern might characterize other mammals currently considered endemic to the CM, we examined which of these species match two criteria that we propose herein to estimate if they can be regarded as endemic to the CM with confidence: (1) that morphological or molecular evidence exists indicating that the putative endemic taxon is distinctive from congeneric populations in the CO; and (2) that the putative endemic taxon is restricted to either cloud forest or páramo, or both. Only Aepeomys reigi, Cryptotis meridensis, and Nasuella meridensis matched both criteria; hence, additional research is necessary to assess the true taxonomic status and distribution of the remaining species thought to be CM endemics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129113PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488270PMC
March 2016
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