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Locomotion performance in reptiles is deeply associated with habitat use, escape from predators, prey capture, and territory defense. As ectotherms, this trait in lizards is extremely sensitive to body temperature (BT). However, most studies rarely look at locomotion patterns in an ontogenic perspective. The Moorish gecko, Tarentola mauritanica, was used to investigate the possible effects of distinct BTs on the locomotor performance within juveniles and adults. Not surprisingly, adult individuals significantly outperform the juveniles in speed at every BT. Moreover, except in the 30-day-old juveniles, there is a general trend for an increase of speed with BT. The comparison of these speed values with the ones obtained for diurnal lizard species, corroborates the premise that because nocturnal species are subject to low thermal heterogeneity, little selection for behavioral thermoregulation, but strong selection for high performance at relatively cool temperatures are expected. Furthermore, the higher locomotor performance in adults at 29°C, roughly coincides with previously obtained preferred BTs. However, further studies need to be conducted to build the full performance curve, and to validate the existence of coadaption between behavioral thermoregulation and thermal sensitivity of physiological performance. Finally, this study has found that adult males run significantly faster than females at the highest BTs, highlighting the importance in understanding sex differences, and its potential to drive sex-specific behaviors, ecology, and ultimately fitness.

La apertura, fiabilidad, identificación e interoperabilidad de la información científica son aspectos cada vez más relevantes para la comunidad científica y la infraestructura abierta de investigación. Dentro de la infraestructura abierta de investigación, uno de los pilares de la Ciencia Abierta, los identificadores persistentes se establecen como un bloque principal, permitiendo la interoperabilidad entre entidades como autores, producción e instituciones. Para consolidar y mantener buenas prácticas en torno a ellos, DataCite y ORCID han trabajado conjuntamente desde su creación y han fomentado el desarrollo de comunidades de práctica en la adopción de identificadores persistentes abiertos. Este texto encuadra los identificadores dentro del marco de la Ciencia Abierta y la FAIRificación de la información científica. Asimismo, presenta la trayectoria conjunta de DataCite y ORCID y el concepto de comunidades de práctica aplicado a identificadores persistentes abiertos. Por último, explora el trabajo desarrollado en Iberoamérica y posibles escenarios futuros.

Similar to other South American regions, Tierra del Fuego has an admixed population characterized by distinct ancestors: Native Americans who first occupied the continent, European settlers who arrived from the late 15th century onwards, and Sub-Saharan Africans who were brought to the Americas for slave labor. To disclose the paternal lineages in the current population from Tierra del Fuego, 196 unrelated males were genotyped for 23 Y-STRs and 52 Y-SNPs. Haplotype and haplogroup diversities were high, indicating the absence of strong founder or drift events. A high frequency of Eurasian haplogroups was detected (94.4%), followed by Native American (5.1%) and African (0.5%) ones. The haplogroup R was the most abundant (48.5%), with the sub-haplogroup R-S116* taking up a quarter of the total dataset. Comparative analyses with other Latin American populations showed similarities with other admixed populations from Argentina. Regarding Eurasian populations, Tierra del Fuego presented similarities with Italian and Iberian populations. In an in-depth analysis of the haplogroup R-M269 and its subtypes, Tierra del Fuego displayed a close proximity to the Iberian Peninsula. The results from this study are in line with the historical records and reflect the severe demographic change led mainly by male newcomers with paternal European origin.

San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions. We thank all sample donors for their contribution to this work and all the people who helped with sample collection, namely, Regina Miranda from the Community of San Basilio de Palenque, the personnel of the Benkos Biojó Rural school, and Miguel Obeso from the etnoeducación program. This work was supported by the University of Cartagena and FPIT—Fundación para la promoción de la investigación y la tecnología del Banco de la República, Colombia (FPIT-388) and partially financed by FEDER—Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the projects “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274). FS was supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro—FAPERJ (E-26/202.275/2019). LG was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico—CNPq (ref. 306342/2019-7), and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro—FAPERJ (CNE-2018). VG was supported by FCT, under the program contract provided in Decree-Law no.57/2016 of August 29. The IPATIMUP integrates the i3S research unit, which is partially supported by the Portuguese Foundation for Science and Technology.

In the already identified quantitative trait loci (QTL), modulating Hb F levels are cis-acting haplotypes of the β-globin gene cluster itself, although the single nucleotide polymorphisms (SNPs) accounting more for the association, remain uncertain. In this study, the role in Hb F production of previously reported candidate SNPs within the β-globin gene cluster was reexamined, along with a yet poorly studied variation in the BGLT3 gene. In a sample of β-thalassemia (β-thal) carriers, we succeeded in replicating the significant association between increased Hb F levels and rs7482144 (C>T) (HBG2 XmnI), which is the most well-established variation in the cluster influencing the trait. This SNP was found to be in strong linkage disequilibrium (LD) with a variation in the HBBP1 gene [rs10128556 (G>A)], which consistently revealed a similar association signal. Remarkably, much stronger than the latter associations were those involving both rs968857 (T allele) (3' HBBP1) and rs7924684 (G allele) (BGLT3), two SNPs that were also in strong LD. As the pattern of LD detected in the β-globin gene cluster does not correlate with a tight linkage between markers, complex interactions between SNPs at the cluster seem to modulate Hb F. Seeing that no such associations were detected in normal subjects, the question can be raised on whether, under erythropoiesis stress, epigenetic mechanisms contribute to change the regulation of the entire β-globin gene cluster. In conclusion, we provide statistical evidence for a new player within the β-globin gene cluster, BGLT3, that in cooperation with other regions influences Hb F levels in β-thal carriers.

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

The widespread observation that heat tolerance is less variable than cold tolerance (‘cold-tolerance asymmetry’) leads to the prediction that species exposed to temperatures near their thermal maxima should have reduced evolutionary potential for adapting to climate warming. However, the prediction is largely supported by species-level global studies based on single estimates of both physiological metrics per taxon. We ask whether cold-tolerance asymmetry holds for Iberian lizards after accounting for intraspecific variation in critical thermal maxima (CT) and minima (CT). To do so, we quantified CT and CT for 58 populations of 15 Iberian lizard species (299 individuals). Then, we randomly selected one population from each study species (population sample = 15 CT and CT values), tested for differences between the variance of both thermal metrics across species, and repeated the test for thousands of population samples as if we had undertaken the same study thousands of times, each time sampling one different population per species (as implemented in global studies). The ratio of variances in CT to CT across species varied up to 16-fold depending on the populations chosen. Variance ratios show how much CT departs from the cross-species mean compared to CT, with a unitary ratio indicating equal variance of both thermal limits. Sampling one population per species was six times more likely to result in the observation of greater CT variance (‘heat-tolerance asymmetry’) than cold-tolerance asymmetry. The probability of obtaining the data (given the null hypothesis of equal variance being true) was twice as likely for cases of cold-tolerance asymmetry than for the opposite scenario. Range-wide, population-level studies that quantify heat and cold tolerance of individual species are urgently needed to ascertain the global prevalence of cold-tolerance asymmetry. While broad latitudinal clines of cold tolerance have been strongly supported, heat tolerance might respond to smaller-scale climatic and habitat factors hence go unnoticed in global studies. Studies investigating physiological responses to climate change should incorporate the extent to which thermal traits are characteristic of individuals, populations and/or species. A free Plain Language Summary can be found within the Supporting Information of this article., Funding from British Ecological Society ‘Research Grant’ 4496-5470 to S.H.-P., and CGL2011-26852 project of the Spanish Ministry of Economy and Competitiveness and IC&DT 1/SAESCTN/ALENT-07-0224-FEDER-001755 to M.B.A.

COMPETE 2020. POCI-01-0145-FEDER-007274 to i3S. Submitted by Maria da Luz Antunes (mluz.antunes@estesl.ipl.pt) on 2019-08-27T10:17:35Z No. of bitstreams: 1 Unusual β-globin haplotype distribution in newborns from Bengo, Angola.pdf: 1300567 bytes, checksum: 707e68d119bc13ff44b0bde94b8ffabc (MD5) Made available in DSpace on 2019-08-27T10:17:35Z (GMT). No. of bitstreams: 1 Unusual β-globin haplotype distribution in newborns from Bengo, Angola.pdf: 1300567 bytes, checksum: 707e68d119bc13ff44b0bde94b8ffabc (MD5) Previous issue date: 2019-08 info:eu-repo/semantics/publishedVersion

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n=31,573) has the highest number of records followed by Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496), Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n=12,159], Monachus monachus [n=1,512], and Lynx pardinus [n=197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications.

To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.

In oviparous species, pesticides may affect embryo survival via maternal transfer or contaminant absorption from the soil, thus representing an important cause of population decline. Maternal transfer is a source of contamination during vitellogenesis and oviductal egg retention. Currently, there is still limited evidence of the potential risk of embryonic exposure routes in reptiles. We investigated whether different agricultural treatments affect embryo, egg, and hatchling development and survival in the Italian wall lizard. We kept gravid females from conventional and control fields in captivity until oviposition and, after eggs being incubated in a pesticide-free environment, offspring morphology and performance (running speed) were assessed. Our results showed that the size of the mother positively influences the number of the eggs and offspring, as well as hatching body condition. Bigger females from conventional treatments tended to lay more eggs. Moreover, at equal female body conditions, eggs and hatchlings from conventional treatments had worse quality (i.e., smaller size and lower body condition) than those from control areas. No effect of treatment was observed on hatchling locomotor performance. In conclusion, our study provided new insights of the direct and indirect effects of field management (i.e., pesticide exposure) on females' reproductive success through the alteration of female's behaviour, which in turn may affect offspring development and health.

Biting performance is important for feeding, territory defense, and mating in many animals. While maximal bite force is a well-studied trait, other aspects of biting and their variation depending on behavior are rarely considered. Here, we took an innovative approach, where (1) we quantified a novel trait, bite duration in lizards; (2) we examined variation across setups that simulate feeding and antagonistic behavior; and (3) we used F-matrix statistics to investigate how different functional components are optimized for ecological and social demands with respect to individual morphology. Our results did not show differences between the sexes in bite duration, but bite performance varied across experimental setups in males, suggesting a higher functional flexibility in this sex. The investigation of form-function associations revealed that trade-offs, facilitations, and one-to-one relationships are simultaneously involved in the morphological optimization of bite force and duration. Put together, our integrated analysis of two different components of bite performance-force and duration-demonstrates their importance for males in both ecological and social tasks. Our findings also suggest the existence of trade-offs in the morphological optimization of functional components, possibly due to physiological constraints on muscle composition, insertion, and orientation.

Numerous studies have demonstrated the ecological and social relevance of different aspects of animal locomotor performance, as locomotion is frequently required to capture prey, escape from predators, find mates and defend territories. Typically, maximal performance is quantified using two alternative methods: across distance intervals or across time intervals, the later by extracting the speed observed between a specified number of video frames. Here, we analyze how this choice may influence statistical inference and the derived biological interpretations. Our results indicate that data obtained using 10-cm intervals are categorized, not normally distributed, exhibit lower individual repeatabilities and have four times more variance compared to the data obtained by quantifying speeds across short time intervals. These results have important methodological implications, as they suggest that the choice of method of speed quantification substantially influences the quality and bias of maximal performance descriptors. This may in turn have a profound influence on ecomorphological inference, as it affects our capacity of detecting variation in performance within and across groups, and associations between locomotor performance and other traits.

Made available in DSpace on 2020-12-12T00:58:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Anaesthetics Research Society The use of Y-chromosomal genetic markers in forensic investigations demands the establishment of reliable and representative DNA databases of different reference populations. The genetic characterization of the Y chromosome variation in human populations requires the analyses of haplotype frequencies allied to haplogroup determination. The present study aimed to contribute to the Brazilian database by providing 1,382 Yfiler Plus individual profiles, from 11 Brazilian states. The Yfiler Plus markers showed high haplotype diversities in all Brazilian populations (>0.9970), allowing high intra-population discrimination in forensic investigations. Pairwise genetic distances showed a homogeneity between Brazilian populations (FST ≤ 0.0043; non-differentiation p-values ≥ 0.0212), indicating that admixed populations from Brazil can be represented in a single Yfiler Plus haplotype database, for forensic purposes. The performance of Haplogroup Predictor and NevGen software in haplogroup prediction based on Yfiler Plus and Yfiler haplotypes was evaluated in a subset of 416 Brazilian samples that were also genotyped for 51 Y-SNPs. In 25% of the samples, no classification or errors were found for at least one of the prediction tools or marker sets. NevGen presented lower error rates (5.52% and 8.65% with Yfiler Plus and Yfiler, respectively) than Haplogroup Predictor (16.11% with Yfiler Plus and 13.70% with Yfiler). In conclusion, both haplogroup prediction tools can be useful to direct the SNP typing, but present large error rates to be used in forensic analysis, especially in predicting African haplogroups in admixed South American populations. DNA Diagnostic Laboratory (LDD) State University of Rio de Janeiro (UERJ) Laboratory of Human and Molecular Genetics Pontifícia Universidade Católica do Rio Grande do Sul Laboratório de Biologia e DNA Forense Superintendência de Polícia Técnico-Científica do Estado de Goiás UNESP-Universidade Estadual Paulista Faculdade de Ciências Farmacêuticas Laboratório de Investigação de Paternidade-NAC Coordenadoria de Perícias em Biologia Molecular POLITEC – Perícia Oficial e Identificação Técnica Faculdade Pitágoras Departamento de Medicina Legal Ética Médica e Medicina Social e do Trabalho da Faculdade de Medicina da USP Universidade de São Paulo (USP) IPATIMUP-Institute of Pathology and Molecular Immunology from the University of Porto I3S-Instituto de Investigação e Inovação em Saúde Universidade do Porto Postgraduate Program in Genetics and Molecular Biology Laboratory of Human and Medical Genetics Federal University of Pará Secretaria de Defesa Social Pernambuco Serviço de Endocrinologia e Metabologia do Hospital Universitário da Universidade Federal do Maranhão UNESP-Universidade Estadual Paulista Faculdade de Ciências Farmacêuticas Laboratório de Investigação de Paternidade-NAC Anaesthetics Research Society: 304413/2015-1

Current and past parasite transmission may depend on the overlap of host distributions, potentially affecting parasite specificity and co-evolutionary processes. Nonetheless, parasite diversification may take place in sympatry when parasites are transmitted by vectors with low mobility. Here, we test the co-speciation hypothesis between lizard final hosts of the Family Lacertidae, and blood parasites of the genus Schellackia, which are potentially transmitted by haematophagous mites. The effects of current distributional overlap of host species on parasite specificity are also investigated. We sampled 27 localities on the Iberian Peninsula and three in northern Africa, and collected blood samples from 981 individual lizards of seven genera and 18 species. The overall prevalence of infection by parasites of the genus Schellackia was ∼35%. We detected 16 Schellackia haplotypes of the 18S rRNA gene, revealing that the genus Schellackia is more diverse than previously thought. Phylogenetic analyses showed that Schellackia haplotypes grouped into two main monophyletic clades, the first including those detected in host species endemic to the Mediterranean region and the second those detected in host genera Acanthodactylus, Zootoca and Takydromus. All but one of the Schellackia haplotypes exhibited a high degree of host specificity at the generic level and 78.5% of them exclusively infected single host species. Some host species within the genera Podarcis (six species) and Iberolacerta (two species) were infected by three non-specific haplotypes of Schellackia, suggesting that host switching might have positively influenced past diversification of the genus. However, the results supported the idea that current host switching is rare because there existed a significant positive correlation between the number of exclusive parasite haplotypes and the number of host species with current sympatric distribution. This result, together with significant support for host–parasite molecular co-speciation, suggests that parasites of the genus Schellackia co-evolved with their lizard hosts., Ministerio de Economía y Competitividad and European Regional Development Fund (MINECO/FEDER) provided financial support (CGL2012-40026-C02-01 and CGL2015-67789-C2-1-P to SM; CGL2012-40026-C02-02 to J. Martínez; CGL2015-64086-P to JGP; CGL2014-53523-P to J. Martín; CGL2008-01522, CGL2012-32459, and CGL2016-76918 to PSF). Partial support to sample in the Guadarrama Mountains was provided to OJR by project CGL2011-30393 conceded to I. de la Riva. Ministerio de Educación, Cultura y Deporte and the European Regional Development Fund (MEC/FEDER) funded JJC and JB (grant CGL2008-00137/BOS). MEC also funded RM-P (BES-2010-038427).

Research addressing the effects of global warming on the distribution and persistence of species generally assumes that population variation in thermal tolerance is spatially constant or overridden by interspecific variation. Typically, this rationale is implicit in sourcing one critical thermal maximum (CTmax) population estimate per species to model spatiotemporal cross‐taxa variation in heat tolerance. Theory suggests that such an approach could result in biased or imprecise estimates and forecasts of impact from climate warming, but limited empirical evidence in support of those expectations exists. We experimentally quantify the magnitude of intraspecific variation in CTmax among lizard populations, and the extent to which incorporating such variability can alter estimates of climate impact through a biophysical model. To do so, we measured CTmax from 59 populations of 15 Iberian lizard species (304 individuals). The overall median CTmax across all individuals from all species was 42.8°C and ranged from 40.5 to 48.3°C, with species medians decreasing through xeric, climate‐generalist and mesic taxa. We found strong statistical support for intraspecific differentiation in CTmax by up to a median of 3°C among populations. We show that annual restricted activity (operative temperature > CTmax) over the Iberian distribution of our study species differs by a median of >80 hr per 25‐km2 grid cell based on different population‐level CTmax estimates. This discrepancy leads to predictions of spatial variation in annual restricted activity to change by more than 20 days for six of the study species. Considering that during restriction periods, reptiles should be unable to feed and reproduce, current projections of climate‐change impacts on the fitness of ectotherm fauna could be under‐ or over‐estimated depending on which population is chosen to represent the physiological spectra of the species in question. Mapping heat tolerance over the full geographical ranges of single species is thus critical to address cross‐taxa patterns and drivers of heat tolerance in a biologically comprehensive way., Spanish Ministry of Economy and Competitiveness, Grant Number: CGL2011-26852; European Union, Grant Number: IC&DT1/SAESCTN/ALENT-07-0224-FEDER-001755; British Ecological Society, Grant Number: 4496-5470; Australian Research Council, Grant/Award Number: DP170101046

A central issue in evolutionary biology is how morphology, performance, and habitat use coevolve. If morphological variation is tightly associated with habitat use, then differences in morphology should affect fitness through their effect on performance within specific habitats. In this study, we investigate how evolutionary forces mold morphological traits and performance differently given the surrounding environment, at the intraspecific level. For this purpose, we selected populations of the lizard Podarcis bocagei from two different habitat types, agricultural walls and dunes, which we expected to reflect saxicolous vs ground-dwelling habits. In the laboratory, we recorded morphological traits as well as performance traits by measuring sprint speed, climbing capacity, maneuverability, and bite force. Our results revealed fast-evolving ecomorphological variation among populations of P. bocagei, where a direct association existed between head morphology and bite performance. However, we could not establish links between limb morphology and locomotor performance at the individual level. Lizards from walls were better climbers than those from dunes, suggesting a very fast evolutionary response. Interestingly, a significant interaction between habitat and sex was detected in climbing performance. In addition, lizards from dunes bit harder than those from walls, although sexual differentiation was definitely the main factor driving variation in head functional morphology. Taking into account all the results, we found a complex interaction between natural and sexual selection on whole-organism performance, which are, in some cases, reflected in morphological variation.

Brazil has a large territory divided in five geographical regions harboring highly diverse populations that resulted from different degrees and modes of admixture between Native Americans, Europeans and Africans. In this study, a sample of 605 unrelated males was genotyped for 17 Y-STRs and 46 Y-SNPs aiming a deep characterization of the male gene pool of Rio de Janeiro and its comparison with other Brazilian populations. High values of Y-STR haplotype diversity (0.9999±0.0001) and Y-SNP haplogroup diversity (0.7589±0.0171) were observed. Population comparisons at both haplotype and haplogroup levels showed significant differences between Brazilian South Eastern and Northern populations that can be explained by differences in the proportion of African and Native American Y chromosomes. Statistical significant differences between admixed urban samples from the five regions of Brazil were not previously detected at haplotype level based on smaller size samples from South East, which emphasizes the importance of sample size to detected population stratification for an accurate interpretation of profile matches in kinship and forensic casework. Although not having an intra-population discrimination power as high as the Y-STRs, the Y-SNPs are more powerful to disclose differences in admixed populations. In this study, the combined analysis of these two types of markers proved to be a good strategy to predict population sub-structure, which should be taken into account when delineating forensic database strategies for Y chromosome haplotypes.

Y chromosome markers have been widely studied due to their various applications in the fields of forensic and evolutionary genetics. In this study, 35 Y-SNPs and 17 Y-STRs were genotyped in 253 males from the State of Espirito Santo, Brazil. A total of 18 haplogroups and 243 haplotypes were detected; the haplogroup and haplotype diversities were 0.7794 and 0.9997, respectively. Genetic distance analysis using the Y-STR data showed no statistically significant differences between Espirito Santo and other admixed populations from Brazil. The classification of paternal lineages based on haplogroups showed a predominant European contribution (85.88 %), followed by African (11.37 %) and Amerindian (2.75 %) contributions.

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material—including other animal species, plants, or microorganisms—is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities. MA, FP, MO, NP, AML and VG are supported by the Portuguese Foundation for Science and Technology (FCT), European RegionalDevelopment Fund (ERDF) and Programa Operacional Potencial Humano,through the grants IF/00955/2014, IF/01356/2012, SFRH/BPD/66071/2009, SFRH/BPD/97414/2013, IF/01262/2014 and SFRH/BPD/76207/2011, respectively. MA was also supported by the “Ramón y Cajal” grant RYC-2015-18241 from the Spanish Government. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. The funders had no role in the preparation of the article.

The Y-STRs have high mutation rates, being useful to discriminate unrelated males. They are widely used in paternity and forensic investigations to study the recent history and migration movements of populations. Recently, the YfilerPlus was released to increase discrimination inside populations, by adding 9 Y-STRs to the previous Yfiler version. The genetic composition of Brazil is known to vary through 5 geopolitical regions: South, Southeast, North, Northeast and Central-west. Therefore, for this study, samples from Maranhao, Espirito Santo, Sao Paulo and Rio Grande do Sul were characterized for the Y-STR markers present in YfilerPlus kit, to evaluate if diversity increases with the enlargement of the Yfiler set, and if significant differences exists among populations. Genetic differentiation analysis did not reveal statistically significant differences in the YfilerPlus haplotype composition of the studied samples. High diversities were observed in all samples for both Yfiler and YfilerPlus marker sets. Inside populations, 20 haplotypes were shared by two individuals for the Yfiler-STRs. This number decreases to 14 when using the 25 Y-STRs from the YfilerPlus. The YfilerPlus demonstrated an increased discrimination power in comparison to the Yfiler kit, being suitable for forensic applications in the studied Brazilian populations, for which data were not yet available.

There is an increasing interest in understanding how species respond to the modifications of habitat attributes in urban areas. Patterns in the occurrence and abundance of small mammal communities in 15 isolated patches of remnant natural and semi-natural habitat of Porto Metropolitan Area (Portugal) were assessed against environmental characteristics (from both the patch and the surrounding matrix) of each patch using multiple regressions and canonical correspondence analysis. Four species of common small mammals were found: wood mouse (Apodemus sylvaticus), greater white-toothed shrew (Crocidura russula), Algerian mouse (Mus spretus) and house mouse (Mus musculus). Our results showed that both relative abundance and species richness were negatively affected by urbanization. The species richness also displayed a negative association with the increase of forest around the patch but relative abundance showed the opposite trend. At the species level, the relative abundance of A. sylvaticus and C. russula showed a negative association with urbanization. Our results reveal that these two species also benefit from a mosaic of habitats and pervious areas in the surrounding matrix. The relative abundance of M. spretus and M. musculus showed a negative effect of forest area around the patch. Understanding how the increase of urbanization affects small mammals will be particularly useful for the managers of urban landscapes, as these animals occupy a pivotal position in the ecosystems.

In this work 118 Nilote male samples were genotyped from Karamoja region, in Northeast Uganda, through 17 Y-chromosomal short tandem repeats (STRs)-DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. A total of 94 different haplotypes were found, where 19 were shared by at least two individuals, and haplotype diversity amounted to 0.9958+/-0.0017. When considering only the nine Y-STRs included in the minimal haplotype (YHRD) the haplotype diversity decreased to 0.9807+/-0.0048, a similar value to those found in other African populations such as Mozambique, Angola and Guinea-Bissau. Population comparisons were performed between our sample and nine other African populations. Significant R(st) genetic distances were obtained between the Nilote population from Karamoja and all African populations used for comparison, except Xhosa sample from South Africa. In the multidimensional scaling (MDS) plot, the Karamoja sample is well separated from all other populations, standing between the Ethiopia and the Bantu samples, although closer to this last group.

The most significant and widely studied remodeling of the African genetic landscape is the Bantu expansion, which led to an almost total replacement of the previous populations from the sub-Saharan region. However, a poor knowledge exists about other population movements, namely, the Nilotic migration, which is a pastoralist dispersal that, contrary to the Bantu expansion, impacted only East African populations. Here, samples from a Ugandan Nilotic-speaking population were studied for 37 Y chromosome-specific SNPs, and the obtained data were compared with those already available for other sub-Saharan population groups. Although Uganda lies on the fringe of both Bantu and Nilotic expansions, a low admixture with Bantu populations was detected, with haplogroups carrying M13, M182 and M75 mutations prevailing in Nilotes together with a low frequency of the main Bantu haplogroups from clade E1b1a-M2. The results of a comparative analysis with data from other population groups allowed a deeper characterization of some lineages in our sample, clarifying some doubts about the origin of some particular Y-SNPs in different ethnic groups, such as M150, M112 and M75. Moreover, it was also possible to identify a new Y-SNP apparently specific to Nilotic groups, as well as the presence of particular haplogroups that characterize Nilotic populations. The detection of a new haplogroup B2a1b defined by G1, could be, therefore, important to differentiate Nilotes from other groups, helping to trace migration and admixture events that occurred in eastern Africa.

The establishment of Jewish communities in the territory of contemporary Portugal is archaeologically documented since the 3rd century CE, but their settlement in Tras-os-Montes (NE Portugal) has not been proved before the 12th century. The Decree of Expulsion followed by the establishment of the Inquisition, both around the beginning of the 16th century, accounted for a significant exodus, as well as the establishment of crypto-Jewish communities. Previous Y chromosome studies have shown that different Jewish communities share a common origin in the Near East, although they can be quite heterogeneous as a consequence of genetic drift and different levels of admixture with their respective host populations. To characterize the genetic composition of the Portuguese Jewish communities from Tras-os-Montes, we have examined 57 unrelated Jewish males, with a high-resolution Y-chromosome typing strategy, comprising 16 STRs and 23 SNPs. A high lineage diversity was found, at both haplotype and haplogroup levels (98.74 and 82.83%, respectively), demonstrating the absence of either strong drift or founder effects. A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non-Jewish populations (R1b1b2-M269, ∼28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a-M267), ∼12%; J2-M172, ∼25%; T-M70, ∼16%] and in consequence Tras-os-Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non-Jewish population. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc.

In this study, 123 unrelated Portuguese Gypsies were analyzed for 15 highly polymorphic autosomal short tandem repeats (STRs). Average gene diversity across the 15 markers was 76.7%, which is lower than that observed in the non-Gypsy Portuguese population. Subsets of STRs were used to perform comparisons with other Gypsy and corresponding host populations. Interestingly, diversity reduction in Gypsy groups compared to their non-Gypsy surrounding populations apparently varied according to an East-West gradient, which parallels their dispersion in Europe as well as a decrease in complexity of their internal structure. Analysis of genetic distances revealed that the average level of genetic differentiation between Gypsy groups was much larger than that observed between the corresponding non-Gypsy populations. The high rate of heterogeneity among Gypsies can be explained by strong genetic drift and limited intergroup gene flow. However, when genetic relationships were addressed through principal component analysis, all Gypsy populations clustered together and was clearly distinguished from other populations, a pattern that suggests their common origin. Concerning the putative ancestral genetic component, admixture analysis did not reveal strong Indian ancestry in the current Gypsy gene pools, in contrast to the high admixture estimates for either Europeans or Western Asians.

Karamoja is a region located in the northeast edge of Uganda where it borders Kenya and Sudan. The majority of inhabitants of this region belong to Karimojong ethnic groups. In this work, we present allele frequencies for 15 STRs included in the AmpF/STR Identifiler kit (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) in 218 unrelated individuals from Karamoja region. Observed genotype distributions for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. When comparing allele frequencies, for each locus, with other five African samples (Equatorial Guinea, Mozambique, Cabinda (Angola), Rwanda and Tanzania) the only population that did not show significant differences with Karamoja (Uganda) was Rwanda.

Plant and animal individuals can have a random, regular, or clustered distribution across space. The analyses of these patterns are important to understand how environment influences the spatial structure of species communities. We studied the local spatial segregation in a lizard community that is composed by four species in Salamanca (Spain). We inferred if habitat and / or competition are segregating factors. We collected a total of 675 records with a high‐accuracy GPS unit. We used Ripley’s K function to determine the distance threshold of clustering of the whole community and of each species separately, Delaunay’s triangulation (using as clustering distance threshold the Nearest Neighbor Index) to identify spatial species’ clusters, and an overlapping analysis (using buffers around species records), as well as a distance comparison analysis (among intra‐species and inter‐species distances), to measure the species’ spatial segregation. The lizard community was distributed in 34 clusters, with 13 composed by only one species and 21 composed by two or more species. Our results indicated that species of the same genus segregated almost totally, inhabiting different habitats; on the other hand, species of different genera presented partial segregation, sharing some habitats. Ground‐dwelling species had partial spatial segregation as they compete for similar habitats. Saxicolous species presented a high degree of spatial segregation due to their different habitat.

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago., This study was supported by Fundacao para a Ciencia e Tecnologia (FCT) and co-financed by the European Social Fund (Human Potential Thematic Operational Programme) through grants SFRH/BPD/76207/2011 (VG) and SFRH/BPD/81986/2011 (RP). PS is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013) and acknowledges FCT/MEC for support to CBMA through Portuguese funds (PIDDAC)-PEst-OE/BIA/UI4050/2014. AS is supported by "Ministerio de Ciencia e Innovacion" (SAF2011-26983), the Plan Galego IDT (EM 2012/045) and the grant from the Sistema Universitario Gallego-Modalidad REDES (2012-PG226) from the Xunta de Galicia. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT, the Portuguese Foundation for Science and Technology. This work is funded by FEDER funds through the Operational Programme for Competitiveness Factors-COMPETE and National Funds through the FCT-Foundation for Science and Technology, under the project "PEst-C/SAU/LA0003/2013". NORTE-07-0162-FEDER-00018-Contributos para o reforco da capacidade do IPATIMUP enquanto actor do sistema regional de inovacao and NORTE-07-0162-FEDER-000067 Reforco e consolidacao da capacidade infraestrutural do IPATIMUP para o sistema regional de inovacao, both supported by Programa Operacional Regional do Norte (ON. 2-O Novo Norte), through FEDER funds under the Quadro de Referencia Estrategico Nacional (QREN). We would like to acknowledge the contribution of Magdalen Awor, Fr. Germano Serra and Iva Gomes for collecting the Karamoja samples. We thank Eric Bridgeland for collecting the Kabale samples, Dr Narcis Kabatereine (Vector Control Division, Uganda Ministry of Health) for the Piida samples, and Abigail Enaburekhan, Sadie Anderson- Mann, Rebecca Cole and Steven Groom for preliminary work on the Kabale and Piida sequences.

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.

Objectives We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. Methods A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci. Results Among J1-M267 individuals (n = 36), five different sub-haplogroups were identified, with the most common being J1a2b2-L147.1 (∼72%), which encompassed the majority of representatives of the J1a2b-P58 subclade. One sample belonged to the rare J1a1-M365.1 lineage and presented a core Y-STR haplotype consistent with the Iberian settlement during the fifth century by the Alans, a people of Iranian heritage. The analysis of J2-M172 Portuguese males (n = 74) enabled the detection of the two main subclades at very dissimilar frequencies, J2a-M410 (∼80%) and J2b-M12 (∼20%), among which the most common branches were J2a1(xJ2a1b,h)-L26 (22.9%), J2a1b(xJ2a1b1)-M67 (20.3%), J2a1h-L24 (27%), and J2b2-M241 (20.3%). Conclusions While previous inferences based on modern haplogroup J Y-chromosomes implicated a main Neolithic dissemination, here we propose a later arrival of J lineages into Iberia using a combination of novel Portuguese Y-chromosomal data and recent evidence from ancient DNA. Our analysis suggests that a substantial tranche of J1-M267 lineages was likely carried into the Iberian Peninsula as a consequence of the trans-Mediterranean contacts during the first millennium BC, while most of the J2-M172 lineages may be associated with post-Neolithic population movements within Europe.