Genetic Structure of American Black Bears in the Desert Southwest of North America

Abstract American black bears (Ursus americanus) have recolonized parts of their former range in the Trans-Pecos region of western Texas after a \u3e40-year absence. Assessment of genetic variation, structuring, gene flow, and dispersal among bear populations along the borderlands of Mexico and Texas is important to gain a better understanding of recolonization by large carnivores. We evaluated aspects of genetic diversity and gene flow for 6 sampling areas of black bears in southwestern North America using genotypic data from 7 microsatellite loci. Our results indicated that genetic diversity generally was high in the metapopulation of black bears in northern Mexico and western Texas. The episodic gene flow occurring via desert corridors between populations in northern Mexico and those in western Texas has permitted the establishment of only moderate levels of genetic structuring. Bayesian clustering analyses and assignment testing depicted the presence of 3 subpopulations among our 6 sampling areas and attested to the generally panmictic nature of bear populations in the borderlands region. The potentially ephemeral nature of the small populations in western Texas and genotypic characteristics of bears recolonizing these habitats attest to the importance of linkages along this portion of the borderlands of the United States and Mexico to effectively conserve and manage the species in this part of its range

Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats

The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

We sought to identify new susceptibility loci for Alzheimer's disease through a staged association study (GERAD+) and by testing suggestive loci reported by the Alzheimer's Disease Genetic Consortium (ADGC) in a companion paper. We undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with P ≤ 1 × 10−5. We tested these variants for association in an independent sample (stage 2). Three SNPs at two loci replicated and showed evidence for association in a further sample (stage 3). Meta-analyses of all data provided compelling evidence that ABCA7 (rs3764650, meta P = 4.5 × 10−17; including ADGC data, meta P = 5.0 × 10−21) and the MS4A gene cluster (rs610932, meta P = 1.8 × 10−14; including ADGC data, meta P = 1.2 × 10−16) are new Alzheimer's disease susceptibility loci. We also found independent evidence for association for three loci reported by the ADGC, which, when combined, showed genome-wide significance: CD2AP (GERAD+, P = 8.0 × 10−4; including ADGC data, meta P = 8.6 × 10−9), CD33 (GERAD+, P = 2.2 × 10−4; including ADGC data, meta P = 1.6 × 10−9) and EPHA1 (GERAD+, P = 3.4 × 10−4; including ADGC data, meta P = 6.0 × 10−10)

A novel Alzheimer disease locus located near the gene encoding tau protein

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordAPOE ε4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ε4+ (10 352 cases and 9207 controls) and APOE ε4- (7184 cases and 26 968 controls) subgroups as well as in the total sample testing for interaction between a single-nucleotide polymorphism (SNP) and APOE ε4 status. Suggestive associations (P<1 × 10-4) in stage 1 were evaluated in an independent sample (stage 2) containing 4203 subjects (APOE ε4+: 1250 cases and 536 controls; APOE ε4-: 718 cases and 1699 controls). Among APOE ε4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 data sets (best SNP, rs2732703, P=5·8 × 10-9). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100-kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ε4+ subjects (CR1 and CLU) or APOE ε4- subjects (MS4A6A/MS4A4A/MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6 × 10-7) is noteworthy, because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P≤1.3 × 10-8), frontal cortex (P≤1.3 × 10-9) and temporal cortex (P≤1.2 × 10-11). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2 × 10-6) and temporal cortex (P=2.6 × 10-6). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ε4 compared with persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted

Organization of repetitive DNA in the primitive reptile (Sphenodon Punctatus) /

no.178 (1998

Genic variation of mainland and island populations of natalus stramineus (chiroptera: natalidae) /

no.171 (1997

Hepatitis E Virus Genotype 3 in Wild Rats, United States

The role of rodents in the epidemiology of zoonotic hepatitis E virus (HEV) infection has been a subject of considerable debate. Seroprevalence studies suggest widespread HEV infection in commensal Rattus spp. rats, but experimental transmission has been largely unsuccessful and recovery of zoonotic genotype 3 HEV RNA from wild Rattus spp. rats has never been confirmed. We surveyed R. rattus and R. norvegicus rats from across the United States and several international populations by using a hemi-nested reverse transcription PCR approach. We isolated HEV RNA in liver tissues from 35 of 446 rats examined. All but 1 of these isolates was relegated to the zoonotic HEV genotype 3, and the remaining sequence represented the recently discovered rat genotype from the United States and Germany. HEV-positive rats were detected in urban and remote localities. Genetic analyses suggest all HEV genotype 3 isolates obtained from wild Rattus spp. rats were closely related

Eligmodontia bolsonensis Mares, Braun, Coyner, Van & Bussche, 2008, new species

Eligmodontia bolsonensis, new species Holotype. OMNH 34739, adult female, collected by J. K. Braun on 8 October 1999 (original field number Arg 4924), skin, skull, skeleton. Type locality. ARGENTINA: Catamarca Province: Pomán: Establecimiento Río Blanco, 28 km S, 13.3 km W Andalgalá 27 ° 51 ’01”S, 66 ° 18 ’ 17 ”W. Distribution. This species is known presently from Catamarca Province, in the area north and west of the Sierra de Ambato and Sierra de Manchao from localities in the Salar de Pipanaco and Campo Arenal, and in the valley system extending north of Belẻn to Laguna Blanca. It also may occur in the valley system extending north-northeast through the Valles Calchaquíes to Cafayate, Salta Province (Lanzone et al. 2007). This area of sand dunes and sand formations is relatively isolated from the Campo de Belẻn and the Salar de Pipanaco to the south by the Sierra de Belẻn. Etymology. bolson—referring to a geographic feature + - ensis (L), adjectival suffix meaning “to belong to.” Named for the region in which it occurs—the Monte de Sierras y Bolsones. Diagnosis. A member of the genus Eligmodontia distinguishable from all other species by the following combination of characters: dorsum light yellowish brown; venter immaculate; tail without pencil and whitish dorsally and ventrally; length of tail greater than length of head and body; darkish band extending from nose to between ears absent; size intermediate between E. moreni and E. typus (Table 5); greatest length of skull generally 23–25 mm; length of maxillary toothrow generally 3.7 –4.0 mm; length of nasals generally 8.7–9.5 mm; anterior border of zygomatic plate generally slightly concave; bullae and eustachian tubes moderately developed; stapedial spines of bullae round or ovoid; knobs at frontoparietal suture well developed; braincase moderately inflated, but auditory bullae visible in dorsal view. Measurement of holotype. External measurements (in mm): total length, 187; length of tail, 102; length of head and body, 85; length of hind foot, 23; length of ear, 16. Weight (in g): 17.5. Cranial measurements (in mm): greatest length of skull, 24.05; condylobasal length, 22.66; interorbital breadth, 3.69; zygomatic breadth, 12.21; breadth of braincase, 11.26; maxillary toothrow length, 3.68; bullar width, 4.81; bullar length, 4.32; palatilar length, 10.25; diastema length, 5.64; palatal bridge length, 4.18; palatal width at M 1, 2.90; nasal length, 8.90; incisive foramen length, 5.23; incisive foramen width, 1.50. See Table 5 for measurements for all specimens examined. Description. Size small as in other species in the genus. Pelage is long and lax. Overall coloration of the dorsum is very pale yellowish brown; hairs are light ochraceous buff for about the distal 1 / 2 and grayish for the proximal 1 / 2; long, dark guard hairs are present giving the dorsum a slightly darker appearance. Venter is immaculate and hairs are white to the base. Transition from dorsum to venter is sharply defined and delineated by a slightly brighter colored line of light ochraceous buff. Area around the nose and mouth is immaculate white. Ears have well-developed whitish pre-auricular tufts and moderately developed post-auricular patches. Fore- and hind feet are covered with whitish hairs; soles are lightly covered with hairs. Hind feet are elongated; hypothenar pad is absent; plantar pads D 2-4 fused. Tail is unicolored, pale white above and below, longer than the length of the head and body, and without a pencil. Skull delicate, rostrum slender, and braincase smooth and rounded (Fig. 5). Nasals not extending beyond premaxillary-frontal suture. Zygomatic arches delicate, parallel, and little expanded. Zygomatic notches moderately deep, greater than 1 / 2 the width of the zygomatic plate. Lacrimals well developed. Supraorbital edges divergent posteriorly, edges square, a distinct knob present at the frontoparietal suture. Frontoparietal suture crescent shaped. Interparietal well developed. Anterior border of zygomatic plate slightly concave. Masseteric tubercules at bases of zygomatic plates well developed. Palate long, extending beyond the posterior plane of M 3. Incisive foramina long, the posterior margin about level with anterolabial and anterolingual conules of M 1. Palatines with 1 or 2 small, round foramina. Posterolateral palatal pits anterior to mesopterygoid fossa. Bullae moderately inflated; eustachian tubes short, not reaching posterior edge of parapterygoid processes. Parapterygoid fossa shallow and broadly expanded laterally. Stapedial spine of auditory bullae rounded or ovoid. Alisphenoid strut present. Foramen ovale, carotid canal, stapedial foramen, and middle lacerate foramen present. Posterior projection of the mandible with a notch (angular notch) not extending anterior to posterior edge of capsular projection. Knob of masseteric ridge exceeds dorsal edge of diastema of mandible. Caudal vertebrae number 30–31, the sacral vertebrae number 3, and the ribs number 13. Upper incisors opisthodont, slender, ungrooved, and pigmented orange (Fig. 5). Maxillary toothrows slightly posteriorly convergent. Primary cusps of molars alternate. M 1 with anteriomedian flexus obsolete or absent. Minor and major labial and lingual folds with lophs and styles absent or obsolete, including protostyle, parastyle, mesostyle, and enterostyle. M 2 with hypoflexus and metaflexus open and lophs and styles absent; paraflexus present and well developed; posteroflexus absent; anteroloph well developed, extending greater than 2 / 3 the width of paracone and present even in well-worn teeth; paracone and metacone larger than protocone and hypocone. M 3 with hypoflexus often present as a small notch; metaflexus distinct or present as an enamel island; anteroloph present, but may be obsolete in worn teeth; m 1 with well-developed procingulum; anterolingual and anterolabial conulids not extending to lingual and labial edges of metaconid and protoconid; posterolophid and posteroflexid present and well developed, the former extending at least halfway to the lingual edge of entoconid; m 2 with anterolabial cingulum, posterolophid, and posteroflexid present, except in worn teeth; m 3 with hypoflexid present. Comparisons. The only species of Eligmodontia currently known to be broadly sympatric with E. bolsonensis is E. moreni. We have collected the two species only a meter apart, with E. bolsonensis preferring soft, sandy substrates and E. moreni being found on the more dense clay and gravelly soils. In areas where E. bolsonensis does not occur, E. moreni is common on the soft, sandy soils. E. moreni may be distinguished by the following: larger size (Table 5); less buffy dorsum; posteriorly divergent band extending from the tip of the nose to between the ears, which appears more distinct due to the light coloration around the eyes; ears generally darker in coloration; bicolored, tufted tail; smaller knobs at the frontoparietal suture; larger bullae; eustachian tubes that extend anteriorly to the parapterygoid processes; narrower middle lacerate foramina; shorter, less developed stapedial spines of bullae flattened or adpressed to bullae; slightly shorter palate, which extends beyond the posterior border of M 3 by the length of M 3; and 2 N= 52, FN= 50. Eligmodontia typus occurs in the general region, but is not known to be sympatric with E. bolsonensis, although we have found several areas of sympatry between E. typus and E. moreni. E. typus may be distinguished by the following: smaller size (Table 5); darker dorsum; posteriorly divergent band extending from the tip of the nose to between the ears, which appears more distinct due to the light coloration around the eyes; general appearance of ears dark; bicolored tail without a tuft; knobs at the frontoparietal suture absent; shorter, wider nasals and rostrum; anterior border of zygomatic plate less concave; and braincase more inflated, the auditory bullae slightly visible in dorsal view. TABLE 5. Measurements (mm) of species of Eligmodontia. Means, sample size, standard deviations, minimum and maximum are given for each measurement. Significant differences (t-test; P<0.05) are indicated as follows: a n. sp. vs. typus; b n. sp. vs. moreni; c typus vs. moreni. continued. Eligmodontia moreni Natural history. Reproductively active individuals were captured in October and November. Females were pregnant with 4, 5, and 7 embryos. Males had scrotal testes from 7 to 11 mm in length. Reproductively inactive males were collected in March and September. Small mammal species captured at several localities with E. bolsonensis include Thylamys pallidior, Tadarida brasiliensis, Abrothrix andinus, Akodon sp., Andalgalomys olrogi, Calomys sp., E. moreni, E. puerulus, Graomys griseoflavus, Phyllotis xanthopygus, Ctenomys sp., Pipanacoctomys aureus, Microcavia australis, and Chaetophractus vellerosus. Remarks. The karyotype reported by Lanzone et al. (2007) of 2 N= 44, FN= 44 containing 1 pair of large metacentric chromosomes, 20 pairs of acrocentric chromosomes, a small submetacentric Y, and an acrocentric X, likely corresponds to this species. This species was listed as Eligmodontia typus marica by Massoia (1976 / 77), as Eligmodontia sp. 1 by Mares et al. (1997), and Eligmodontia marica by Lanzone et al. (2007). Paratypes. Fourteen specimens collected at or near the type locality; 8 deposited in the OMNH (OMNH 34735, OMNH 34736, OMNH 34737, OMNH 34738, OMNH 34811, OMNH 34812, OMNH 34813, OMNH 34814) and 6 deposited in the CML (field numbers Arg 4914, Arg 4918, Arg 4923, Arg 4926, Arg 4928, Arg 4929). Specimens examined (19). See Appendix 1. Other referred specimens. ARGENTINA: Catamarca: Antofagasta de la Sierra: Pasto Ventura (OMNH 34726 /Arg 5200); 1.5 km S El Peñỏn (OMNH 34725 /Arg 5319). Belẻn: Agua de Dionisio, Hualfín 1 (CML 872); 17 km N Barranca Larga OMNH 34727 /Arg 4954, OMNH 34728 /Arg 4964); 5.2 km S El Bolsỏn (OMNH 34729 /Arg 5168, OMNH 34730 /Arg 5169); Laguna Blanca (OMNH 34731 /Arg 5025, OMNH 34732 /Arg 5026); 1.7 km S Laguna Blanca (OMNH 34734 /Arg 5175, OMNH 34733 /Arg 5176); La Salamanca, Hualfín (Massoia 1976 / 77); Los Baños Termales, Hualfín, 3 (CML 868, 869, 881); Pozo Jovita, Hualfín, 1 (CML 875; Massoia 1976 / 77). Santa María: 21 km SW El Desmonte (OMNH 34743 /Arg 4501); 33 km SW, 1 km N El Desmonte, 1 (OMNH 22303); 7.9 km W jct. Hwy 47 and 40 (OMNH 34806 /Arg 4931, OMNH 34742 /Arg 4932, CML /Arg 4933, CML /Arg 4934, CML /Arg 4935, CML /Arg 4936, OMNH 34807 / Arg 4937, OMNH 34808 /Arg 4938, OMNH 34809 /Arg 4939, OMNH 34810 /Arg 4940, CML /Arg 4941, CML /Arg 4942, CML /Arg 4943, CML /Arg 4944); 9.9 km W jct. Hwy 47 and 40 (OMNH 34740 /Arg 4946, OMNH 34741 /Arg 4947, CML /Arg 4949).Published as part of Mares, Michael A., Braun, Janet K., Coyner, Brandi S., Van, Ronald A. & Bussche, Den, 2008, Phylogenetic and biogeographic relationships of gerbil mice Eligmodontia (Rodentia, Cricetidae) in South America, with a description of a new species, pp. 1-33 in Zootaxa 1753 on pages 15-19, DOI: 10.5281/zenodo.18174

Current potential suitable habitat for the common vampire bat, <i>Desmodus rotundus</i>. based on four different environmental data sets.

<p>(A) present, (B) 2030, (C) 2050, (D) 2080. Black dots indicate spatially unique known occurrences for <i>D. rotundus</i> which were used in model construction.</p