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Simple Summary: Calves should be regularly weighed to monitor their growth, which can be an indication of their health and welfare. Pre-weaned calves are particularly vulnerable to health problems as their immune system is still developing. In addition, knowing the calf's weight can help to provide a more balanced diet and to be more accurate when administering medication. However, there are still many farmers who do not have a scale on their farm or who have limitations in weighing their calves. Therefore, we developed a model using morphometric traits to estimate the weight of Holstein–Friesian pre-weaned calves without the need for a scale, which should be easy to use in most circumstances. Our model used the measurement of heart girth with a simple tape measure and was able to predict the weight of the calf with a mean difference of −1.4 ± 3.24 kg from the actual weight. We did not find any differences between females and males, but we did find differences between farms, which could be due to different genetic lines associated with farm breeding protocols. In addition, a web application was developed to make it easy for farmers to use the developed model. This avoids the use of calibrated weight bands, which are usually calibrated for a wider age range or for beef breeds. Regularly weighing calves helps to assess the efficiency of the rearing period and contributes to animal welfare by allowing more precise feeding and medication application in dairy farming, but many farmers do not weigh their calves regularly. Improving the feasibility of this process is, therefore, important. The use of morphometric measurements has been used to estimate the weight of cattle. However, many studies have focused on adult animals or used a wide age range. As calves experience allometric tissue growth, specific models for certain ranges might be more accurate. Therefore, the aim of this work was to develop a weight estimation model specific for pre-weaned Holstein–Friesian calves using morphometric measurements and to compare the model with another equation previously validated for the same breed with young and adult animals. From four dairy farms, 237 measurements of body weight, heart girth, abdominal girth, hip height, withers height, and body length were taken from Holstein–Friesian male and female calves. Linear and non-linear regression analysis was used to test the relationship between body weight and morphometric measurements, with age, sex, and farm as possible explanatory variables. Selected models were compared with goodness of fit and agreement tests. The final model was able to accurately predict body weight (R2 = 0.96) with a mean difference of −1.4 ± 3.24 kg. Differences in the relationship between body weight and morphometric traits were observed between farms, but not between males and females. The genetics of the animal population at farm level may be responsible for this variability and further studies are needed to understand this variability and improve weight prediction models. The developed model was able to perform better in the agreement tests than the previously validated model for Holstein–Friesian animals, suggesting that different equations should be used depending on the growth phase the animal is in. In addition, a web application has been developed to facilitate the use of the developed model by farmers. This avoids the use of calibrated weight bands, which are usually calibrated for a broader age range or for beef cattle. [ABSTRACT FROM AUTHOR]

Sex determination by DNA-based molecular techniques in Sumatran tigers needs to be investigated and developed for forensic and population genetic purposes. The amelogenin gene is a marker commonly used for sex determination. In some species, the difference between the AMELX and AMELY sequences has been reported to be in the intron region. However, the difference between the AMELX and AMELY sequences in the Sumatran tiger is unknown. Therefore, it is necessary to investigate the sequence differences in introns between AMELX and AMELY Sumatran tigers to determine the specific differences between male and female samples. This study aimed to analyse the sequence of nucleotide bases in the Sumatran tiger amelogenin gene introns based on the nucleotide base sequences in the amelogenin gene introns. The method in this research is descriptive, with a molecular observation of the AMELX and AMELY Sumatran tiger sequences. The amplified samples were sequenced, and it was found that the lengths of the AMELX and AMELY Sumatran tiger sequences were 215 bp and 194 bp, respectively, with a 21 bp deletion in the AMELY sequence. [ABSTRACT FROM AUTHOR]

The Start Codon Targeted Polymorphism (SCoT) and CAAT box-derived polymorphism (CBDP) techniques were used to analyze the genetic diversity and variation of two bigfin reef squid populations in waters surrounding the Con Dao and Phu Quoc islands of Vietnam for technical comparison. The two used techniques reflected different levels of pairwise genetic similarity among individuals depended on the investigated population. Gene differentiation (GST) between the two investigated populations was 0.0767 and 0.0373 leaded to the genetic distance between them was 0.0381 and 0.0228, and the gene flow was Nm = 6.0195 and 12.9061 migrants per generation between the populations based on SCoT and CBDP techniques, respectively. Genetic variation within individuals of both populations (WP) played the key role in the total genetic variation of whole species in surveyed geographic regions with the distribution of 91.44% based on SCoT data and 93.76% based on CBDP data, the distribution of genetic variation among populations (AP) was small. For whole species in the surveyed region, the CBDP markers showed higher genetic diversity, while the SCoT markers reflected the differentiation and genetic distance between the two investigated populations better. Overall, the abilities to detect polymorphisms and the number of revealed loci using SCoT markers were better than using CBDP markers, while the ability to distinguish samples and the primer combination to detect the differences among investigated samples using CBDP markers were better than using SCoT markers, and the overall utility was comparable between these two marker systems. The results from this study prove that the CBDP technique can also be used in studies of animal population genetics. [ABSTRACT FROM AUTHOR]

The article focuses on the ecological impact of genetic processes in a keystone predator species, specifically grey wolves. It is reported that the study assesses how changes in the genetic characteristics of the wolf population on Isle Royale National Park over two decades has affected the ecosystem. It demonstrates how genetic changes in the wolf population, including a genetic rescue event and subsequent inbreeding, influenced predation rates on moose, and the primary prey of wolves.

Keywords: arbuscular mycorrhizal fungi; biogeography; microbial niches; plant-soil interactions; Profile EN arbuscular mycorrhizal fungi biogeography microbial niches plant-soil interactions Profile 330 332 3 09/28/22 20221015 NES 221015 What inspired your interest in plant science? Deciphering the role of specialist and generalist plant-microbial interactions as drivers of plant-soil feedback. i John Davison is an Associate Professor of Plant Ecology at the University of Tartu, Estonia. [Extracted from the article]

Eld's deer (Rucervus eldii) with three recognised subspecies (R. e. eldii, R. e. thamin, and R. e. siamensis) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of R. e. eldii using 19 microsatellite markers. Our results showed that R. e. siamensis exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1–0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between R. e. eldii and R. e. siamensis occurred around 0.4 Mya (95% HPD 0.3–0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore, R. e. eldii exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7–10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld's deer and other species of the genus Rucervus, we propose to classify Eld's deer (Cervus eldii) in the genus Cervus, which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies. [ABSTRACT FROM AUTHOR]

Spermatogonial stem cell transplantation (SSCT) is an experimental technique for transfer of germline between donor and recipient males that could be used as a tool for biomedical research, preservation of endangered species, and dissemination of desirable genetics in food animal populations. To fully realize these potentials, recipient males must be devoid of endogenous germline but possess normal testicular architecture and somatic cell function capable of supporting allogeneic donor stem cell engraftment and regeneration of spermatogenesis. Here we show that male mice, pigs, goats, and cattle harboring knockout alleles of the NANOS2 gene generated by CRISPR-Cas9 editing have testes that are germline ablated but otherwise structurally normal. In adult pigs and goats, SSCT with allogeneic donor stem cells led to sustained donor-derived spermatogenesis. With prepubertal mice, allogeneic SSCT resulted in attainment of natural fertility. Collectively, these advancements represent a major step toward realizing the enormous potential of surrogate sires as a tool for dissemination and regeneration of germplasm in all mammalian species. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Widespread Amazonian taxa are generally found to be many species upon in-depth investigation. • Gecko lizards rarely possess large geographic ranges. • The dwarf gecko, Gonatodes humeralis , is a single species across Amazonia. • Nominal G. humeralis is composed of two sister species. • G. ferrugineus , sister species of G. humeralis , arose allopatrically on the island of Trinidad. Abstract Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. As such, it is rare to find groups that exhibit both large and small ranges. Once identified, however, these groups provide a powerful system for isolating specific traits that influence species distributions. One group of terrestrial vertebrates, gecko lizards, tends to exhibit small geographic ranges. Despite one exception, this applies to the Neotropical dwarf geckos of the genus Gonatodes. This exception, Gonatodes humeralis , has a geographic distribution almost 1,000,000 km2 larger than the combined ranges of its 30 congeners. As the smallest member of its genus and a gecko lizard more generally, G. humeralis is an unlikely candidate to be a wide-ranged Amazonian taxon. To test whether or not G. humeralis is one or more species, we generated molecular genetic data using restriction-site associated sequencing (RADseq) and traditional Sanger methods for samples from across its range and conducted a phylogeographic study. We conclude that G. humeralis is, in fact, a single species across its contiguous range in South America. Thus, Gonatodes is a unique clade among Neotropical taxa, containing both wide-ranged and range-restricted taxa, which provides empiricists with a powerful model system to correlate complex species traits and distributions. Additionally, we provide evidence to support species-level divergence of the allopatric population from Trinidad and we resurrect the name Gonatodes ferrugineus from synonymy for this population. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The Andean and the Atlantic forests acted as refugia. • The main link between the Andean and Atlantic forests occurred through the Cerrado region. • We suggest to split the Buff-browed Foliage-gleaner into two different species (Syndactyla rufosuperciliata and S. cabanisi). Abstract We evaluated whether the Andean and the Atlantic forests acted as refugia during the Quaternary, and tested biogeographic hypotheses about the regions involved in the connectivity between those biomes (through the Chaco or the Cerrado). To achieve these goals we selected the Buff-browed Foliage-gleaner Syndactyla rufosuperciliata (Aves, Furnariidae) as a study system, a taxon distributed between the Andean and Atlantic forest. We first explored the historical connectivity between regions through niche modeling. We subsequently used DNA sequences (n = 71 individuals) and genomic analyses (ddRADseq, n = 33 individuals) to evaluate population genetic structure and gene flow within this species. Finally, we performed population model selection using Approximate Bayesian Computation. Our findings indicate that the Andean and the Atlantic forests acted as refugia, and that the populations of the focal species from both regions contacted through the Cerrado region, thus suggesting that the historical dynamics of Andean and Atlantic forests are important for the evolution of forest birds in the region. The results are in agreement with studies of other organisms and may indicate a more general pattern of connectivity among biomes in the Neotropics. Finally, we recommend recognizing both the Andean and the Altantic forests lineages of S. rufosuperciliata as independent species. [ABSTRACT FROM AUTHOR]

The giant panda is an example of a species that has faced extensive historical habitat fragmentation, and anthropogenic disturbance and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health, and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra‐microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Nonspatial and spatial capture–recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153–175 and 115–163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with four giant panda road‐crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution pose a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta‐population in both Wolong and throughout their current range. We employed noninvasive molecular genetic methods in Wolong Nature Reserve to investigate the giant panda populations in the Northern Qionglai Mountains, with a particular focus on connectivity. Surprisingly, we found that a major road and historical human settlement and agriculture in the valley have not resulted in genetic differentiation between populations on either side of the disturbance. The high levels of migration and gene flow across areas of anthropogenic disturbance found in our study suggest that giant panda populations likely do not face the levels of population isolation within mountain ranges that have been widely assumed. [ABSTRACT FROM AUTHOR]

To address factors affecting genetic diversity and dispersal of ectoparasites, we compared mitochondrial DNA (mtDNA) population genetic structures of the generalist soft tick Ornithodoros capensis to the more host-specific nest flea Parapsyllus humboldti. A total of 103 ticks and 92 fleas were sampled at five distinct South African island/mainland African penguin (Spheniscus demersus) colonies. With its wide host range, O. capensis showed no evidence of significant cytochrome c oxidase subunit I (COI) mtDNA population differentiation among the five sampling sites (φst = 0.00 ± 0.004; p = 0.80), as well as a higher level of genetic diversity (π = 0.8% ± 0.06%) when compared to P. humboldti. In contrast, the flea showed significant population structure among most of the same sampling sites (φst = 0.22 ± 0.11; p ≤ 0.05) and a lower level of genetic diversity (π = 0.2% ± 0.01%). Our findings suggest that despite both parasites being mostly nest bound, O. capensis have few barriers to dispersal among island and mainland colonies. However, P. humboldti are more dependent on the African penguin for dispersal and thus have more impediments to gene flow among the same colonies. These findings broadly support the SGVH (specialist generalist variation hypothesis) and provide the first evidence for this hypothesis in parasites restricted to seabird colonies. [ABSTRACT FROM AUTHOR]

Banija spotted pig breed was created at the end of 19th century by crossing domestic white sows with drooping ears and/or Turopolje pig sows with black Berkshire. After a period of stagnation in breeding, the population is newly recognized only few years ago and is currently in the process of breed valorisation. The aim of this study was to assess genetic diversity and structure of Banija spotted pig (BS) in comparison with geographically close populations, and to assess the differentiation level of Banija spotted pig. Based on the genotypes obtained for 24 ISAG-FAO recommended pig microsatellite markers, basic genetic diversity indicators were determined for 30 samples of BS, 20 samples of Turopolje and Crna Slavonska pig each, and 17 samples of Landrace population. Observed heterozygosity ranged from 0.36 to 0.6 and was high in BS population (0.58). Average allelic richness (range 2 - 5.2) and the rarefacted number of private alleles (range 9 to 27) were the highest in BS. Inbreeding coefficient in BS was estimated 0.06 (bootstrapping confidence interval 0.022 to 0.123). Structure analysis showed that there are five clusters in the four analysed populations, where BS are clearly distinguished from other populations and substructured. Wright's fixation index estimates are in accordance with the clustering results. In conclusion, the population of Banija spotted pig shows great genetic diversity and is genetically different from neighbouring (geographically close) pig populations. [ABSTRACT FROM AUTHOR]

Pareuchiloglanis sinensis (Siluriformes: Sisoridae) is an endemic and highland fish species which occurs only in some rivers of south-west China. In this study, the isolation and characterization of polymorphic microsatellite loci of this fish species by next-generation sequencing is described. A total of 9471 simple-sequence repeats (SSRs) were observed from RNA-seq data. One hundred and twenty primer pairs were chosen randomly and validated across 48 P. sinensis individuals collected from the Dadu river (a branch of the Yangtze river) of which 28 polymorphic microsatellite loci were detected. The number of alleles ranged from 2 to 14, with an average of seven alleles per locus. Twenty loci exhibited high polymorphism with the polymorphism information content (PIC) larger than 0.5. The mean observed and expected heterozygosity varied from 0.104 to 0.958 and 0.157 to 0.844, with an average of 0.583 and 0.613, respectively. The microsatellite markers characterized in the current study serve as a useful tool for the conversation genetic studies and population evaluation of P. sinensis. [ABSTRACT FROM AUTHOR]

Summary: The aim of the present study was to perform a preliminary analysis of the characterization and diversity of Y‐chromosome haplotypes/haplogroups in yak of Qinghai Province, China. A total of 322 male yaks from nine populations belonging to three officially recognized breeds (Gaoyuan, Huanhu and Datong) were sampled. Animals were genotyped using six previously reported Y‐SNPs present in the SRY,USP9Y,UTY,AMELY and OFD1Y genes and four new Y‐SNPs in the OFD1Y gene (g.569A>C, g.578A>C, g.608G>T and g.653G>C) identified in this study. Seven Y‐chromosome haplotypes (H1–H7) were identified according to the combination of the 10 Y‐SNPs. H1, H2 and H6 were the most common and shared haplotypes across all yak populations/breeds. Private haplotypes H3 and H7 were detected in the Datong breed; H4 in Guoleimude, Qumalai, Qilian, Tianjun and Ganglong populations; and H5 in Qumalai of Gaoyuan breed. Haplotype clustering and network analyses inferred two haplogroups, Y1 and Y2, indicating two divergent lineages of paternal origins of Qinghai yak. The analysis of molecular variance showed a significant difference among individuals (P < 0.0001) with more than 93% of the total genetic variation present within populations, suggesting a weak genetic structure among Qinghai yak populations. The overall Y‐haplotype diversity was 0.538 ± 0.028, showing a relatively high diversity in Qinghai yak. The Gaoyuan and Datong breeds had similar haplotype diversities (0.547 ± 0.030 and 0.553 ± 0.083, respectively), which were higher than that of the Huanhu breed (0.441 ± 0.098). Our results support the conservation and sustainable use of unique yak genetic resources in Qinghai. [ABSTRACT FROM AUTHOR]

Abstract: The paper reports the first study of genetic diversity of the domestic yak in the Sayan-Altai region of Russia (Altai and Tuva) and Mongolia (Khuvsgul and Gobi) on the basis of the polymorphism analysis of the mtDNA D-loop hypervariable region. It has been demonstrated that, among all the studied populations, Tuva yaks are characterized by the highest haplotype diversity. Four new haplotypes, A4, A13, D9, and E3, have been described for the first time. The analysis of the contribution of maternal genetic component to the yak intrabreed and interbreed mtDNA diversity revealed two large clades. For the first time, comparative analysis of genetic structure of the Russian yak populations was carried out using 15 microsatellite loci. Low genetic difference between the populations was revealed, which may apparently be accounted for by the specific features of farm breeding, in particular, by animal exchange between the adjacent territories of the Sayan-Altai region. [ABSTRACT FROM AUTHOR]

The red imported fire ant is a well-studied pest in the southern United States, but investigations of invasions in the central region are relatively rare. We compared two central Oklahoma invasions: a newly observed urban invasion on the campus of the University of Central Oklahoma, and an established invasion around Lake Arcadia. We genotyped the General protein-9 (Gp-9) locus to determine social form and eleven microsatellites to evaluate population structure. We hypothesized that colonies were polygyne, that the repeated introductions required to reach central Oklahoma would lead to low genetic diversity, and that the two sites were independently colonized and, therefore, would be genetically isolated. As expected, the analysis of 33 sampled colonies showed that almost all were polygyne and exhibited low genetic diversity, although comparable to diversity found in previous studies. Contrary to our original hypothesis, we discovered that the two separate invasion sites of our study are not differentiated from each other. We found no evidence of distinct genetic clusters within or across sites. However, we did find evidence of two or more introductions that have become integrated. The potential for contemporary gene flow near the northern edge of the fire ant range is concerning as it allows for the maintenance of genetic variation that can lead to more effective adaptation to new environments. [ABSTRACT FROM AUTHOR]

Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil‐stored seed banks as natural archives, in part because of concerns over nonrandom attrition and mixed stratification. Here, we examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records of demographic and population genetic variation. After assembling profiles of the seed bank from radionuclide‐dated soil cores, we germinated seeds to "resurrect" cohorts spanning the 20th century. Using microsatellite markers, we assessed genetic diversity and differentiation among depth cohorts, drawing comparisons to extant plants at the study site and in nearby and more distant marshes. We found that seed density peaked at intermediate soil depths. We also detected genotypic differences among cohorts as well as between cohorts and extant plants. Genetic diversity did not decline with depth, indicating that the observed pattern of differentiation is not due to attrition. Patterns of differentiation within and among extant marshes also suggest that local populations persist as aggregates of small clones, likely reflecting repeated seedling recruitment and low immigration from admixed regional gene pools. These findings indicate that persistent and stratified soil‐stored seed banks merit further consideration as resources for reconstructing decadal‐ to century‐long records that can lend insight into the tempo and nature of ecological and evolutionary processes that shape populations over time. [ABSTRACT FROM AUTHOR]

The asterinid seastars Parvulastra parvivipara and P. vivipara share atypical viviparous reproductive modes that have made them of interest for research on life-history evolution and population genetics. This article briefly reviews life-history traits of these endemic Australian species and information on distribution and rarity, as well as providing some additional new analysis. Almost exclusive self-fertilisation has led to extreme genetic poverty in both species and viviparity limits dispersal potential causing relatively small geographical ranges. There is some evidence that the number of intertidal boulder-fields harbouring P. parvivipara, and the overall geographical range, may have become reduced in recent years. In addition, approximately 25 % of boulder-fields with P. parvivipara have been colonised by invasive oysters (Magallana gigas). To understand potential effects of oysters on P. parvivipara, we tested for correlations between P. parvivipara abundances and cover of oyster encrustations that included this invader (native + non-native oyster shells were assessed together because they produced similar encrustations and largely could not be differentiated). Linear regression showed no evidence, however, for any correlation. For P. vivipara, population survey data from the mid 1970's to present shows marked decline in areas of previous abundance. Parallel with this decline, the boulder habitat has experienced infill and siltation and cementing of the substratum by M. gigas, sponges and other encrusters as well as anoxia. Important future research outcomes on consequences of atypical life-history traits may be allowed by continued research on these seastars but only if their populations are able to persist within the small number of boulderfields where they occur. Current trends may indicate a need for conservation intervention. [ABSTRACT FROM AUTHOR]

Cryptoprocta ferox , or fosa, is the largest living endemic carnivoran of Madagascar, with presumably high dispersal capacity, and for which no broad scale phylogeographic study has been conducted to date. This species is considered “Vulnerable” by the IUCN and the subject of a captive breeding program; approximately 113 individuals are held in 57 zoos. The aim of this study was to examine the genetic structure and polymorphism within both captive and wild populations, to determine possible lineage variation, and to make recommendations for the captive breeding program. For this purpose, we analyzed three mitochondrial (Cytochrome b, ND2, Control Region) and one nuclear (Beta-fibrinogen intron 7) markers. The results showed an overall low level of genetic polymorphism, likely related to its dispersal capacity, and some genetic structure possibly associated with geographical barriers, such as large rivers. The genetic diversity of the captive population was greater than that of wild individuals included herein, suggesting that the captive population encompasses a considerable proportion of the genetic diversity of the species. This genetic variability is presumably the consequence of frequent imports of wild animals into zoos from different areas of Madagascar, and subsequent exchanges between zoos. Based on the low overall genetic polymorphism of the species and the absence of deeply divergent lineages, we recommend the continued mixing of captive animals. Our results may help the management of the fosa in the wild and in captivity, which is crucial for a species that faces many threats in the wild, in particular habitat degradation and hunting pressure. In any case, enhanced protection of the species and its forested habitat is urgently needed. [ABSTRACT FROM AUTHOR]

Genetic relationships between wild boar populations in the southern regions of Iran still remain unclear. Therefore in the present study our aim was filling this gap and providing preliminary knowledge about the phylogenetic status of Iranian wild boar based on two datasets of the mtDNA control region (the 402-bp and 605-bp segments as the first and second datasets, respectively). Altogether 1063 and 490 sequences were used in the shorter and longer sequences, respectively (29 own samples and 1034 and 461 Genbank sequences from previous studies in the first and second datasets, respectively). Our findings revealed that the wild boars living in Southern Iran belong to the previously described three clades: Asian, Near Eastern 1 (NE1) and Near Eastern 2 (NE2) clades. The NE1 and NE2 clades sympatrically occupy a wide range across the southeast to southwest of Iran, whereas the Asian clade is restricted to a small area in the southeastern part of Iran. Our results propose the existence of a contact zone between the Near Eastern clades and the Asian clade in the studied area. The fixation index ( F ST ) and the analysis of molecular variance (AMOVA) demonstrated significant genetic structure among the identified clades. Some identified haplotypes have a wide distribution, which suggests that they are probably ancestral haplotypes or are likely to be a result of recent population expansion. Overall, current research demonstrates that Iranian wild boars have an important phylogenetic position among the others in the world. In other words, Iran is a very important region for addressing some of the topical questions about phylogenetic relationships among the Eurasian wild boar clades. [ABSTRACT FROM AUTHOR]

Abstract: The ecological effects of climate change have been shown in most major taxonomic groups; however, the evolutionary consequences are less well‐documented. Adaptation to new climatic conditions offers a potential long‐term mechanism for species to maintain viability in rapidly changing environments, but mammalian examples remain scarce. The American pika (Ochotona princeps) has been impacted by recent climate‐associated extirpations and range‐wide reductions in population sizes, establishing it as a sentinel mammalian species for climate change. To investigate evidence for local adaptation and reconstruct patterns of genomic diversity and gene flow across rapidly changing environments, we used a space‐for‐time design and restriction site‐associated DNA sequencing to genotype American pikas along two steep elevational gradients at 30,966 SNPs and employed independent outlier detection methods that scanned for genotype‐environment associations. We identified 338 outlier SNPs detected by two separate analyses and/or replicated in both transects, several of which were annotated to genes involved in metabolic function and oxygen transport. Additionally, we found evidence of directional gene flow primarily downslope from high‐elevation populations, along with reduced gene flow at outlier loci. If this trend continues, elevational range contractions in American pikas will likely be from local extirpation rather than upward movement of low‐elevation individuals; this, in turn, could limit the potential for adaptation within this landscape. These findings are of particular relevance for future conservation and management of American pikas and other elevationally restricted, thermally sensitive species. [ABSTRACT FROM AUTHOR]

Abstract: Aim: Tapinoma melanocephalum is listed as one of the most important invasive pest species in China. Information regarding the patterns of invasion and effects of geographic isolation on the population genetics of this species is largely lacking. Location: South China. Methods: To address this problem, we genotyped 39 colonies (two colonies were collapsed due to genetic similarity) using microsatellite markers and mitochondrial DNA sequencing to compare colony genetic structure of T. melanocephalum on the mainland and islands of South China. Results: An analysis of the colony genotypes showed that the genetic diversity of the mainland population was slightly higher than that of the island populations but not significantly so. However, the observed heterozygosity on Shangchuan Island (SCD) was significantly lower than that of the other colonies. We also found six haplotypes in 111 mitochondrial DNA COI sequences. The relatedness (r) value between colonies of SCD was 0.410, higher than that of the other populations. The genetic clusters among colonies were not related to geographic locations and exhibited admixture likely due to frequent human‐mediated dispersal associated with trade between the mainland population and the islands. Pairwise FSTs between populations showed differentiation among mainland populations, while SCD displayed high levels of divergence (FST > 0.15) from most mainland populations. There was no significant isolation by distance among colonies. Most populations showed signs of a bottleneck effect. Main conclusions: Our study suggests that there was no significant difference in the genetic diversity among the islands and the mainland; however, the lower genetic diversity, the higher degree of genetic divergence from other colonies, and the higher relatedness among nestmates made the SCD population stand out from all the others. [ABSTRACT FROM AUTHOR]

Abstract: To date, osteometric data for Swiss Bronze Age cattle, particularly from Alpine sites, are scarce. In the present study, using a large dataset generated by combining preexisting data with recent data obtained from a large Alpine site, cattle size from the Late Neolithic to the Late Bronze Age (LBA) in populations from different sites and regions was evaluated using the logarithmic size index and other statistical analysis. Additionally, the finite mixture model and a meta‐analytic technique were used to observe possible effects of sex ratios on cattle size. Results indicated that sex ratios did not affect size distribution. Cattle populations did not differ over time, but the Alpine cattle were smaller than the Central Plateau cattle. There were two distinct sizes in the Alpine cattle populations. It is suggested that the different economic interrelationships between Alpine and other geographically related communities might have led to the emergence of size diversity in Swiss Bronze Age cattle. Further interdisciplinary studies with larger sample sizes are required to confirm these possibilities. [ABSTRACT FROM AUTHOR]

Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures – theoretical prerequisites for the response to selection. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selection. These biological mechanisms can accelerate or constrain this response. These mechanisms are generally studied independently but might act simultaneously. We therefore integrated these mechanisms to explore their potential combined effect. This has implications for explaining the apparent evolutionary stasis of wild populations and the conservation of wildlife. [ABSTRACT FROM AUTHOR]

Copy number variation (CNV) represents a major source of genomic variation. We investigated the diversity of CNV distribution using SNP array data collected from a comprehensive collection of geographically dispersed sheep breeds. We identified 24,558 putative CNVs, which can be merged into 619 CNV regions, spanning 197 Mb of total length and corresponding to ~ 6.9% of the sheep genome. Our results reveal a population differentiation in CNV between different geographical areas, including Africa, America, Asia, Southwestern Asia, Central Europe, Northern Europe and Southwestern Europe. We observed clear distinctions in CNV prevalence between diverse groups, possibly reflecting the population history of different sheep breeds. We sought to determine the gene content of CNV, and found several important CNV-overlapping genes ( BTG3 , PTGS1 and PSPH ) which were involved in fetal muscle development, prostaglandin (PG) synthesis, and bone color. Our study generates a comprehensive CNV map, which may contribute to genome annotation in sheep. [ABSTRACT FROM AUTHOR]

Octopus minor (Sasaki, 1920) is an important economic fishery resource in China. In order to explore the stock information and the phylogeographic status of O. minor, mitochondrial DNA cytochrome c oxidase subunit I (COI, 565 bp) and 16S rRNA (493 bp) genes were amplified from 11 different sampling locations. Genetic diversity evaluated by haplotypic and nucleotidic diversity implied high diversity in Lianjiang, and relatively low diversity in Rongcheng, which suggests that effective measures to protect the O. minor resource in this area are urgently required. Private haplotypes and remarkable higher pairwise ΦST in Yilan are responsible for the deep genetic divergence between Yilan and the 10 other populations. Haplotypes networks and two clusters’ topological structure also support the distinct subgroups (lineages A and lineages B), which apparently possess smaller genetic variation than mean interspecies distance. Taiwan island and its strait may act as a natural barrier that restricts the gene flow from the mainland. Deep genetic divergence between mainland and Taiwanese east coasts suggests different genetic stock, indicating that different management strategies are required. [ABSTRACT FROM AUTHOR]

Genetic characteristics of the allele pool of four groups of the Yakut snow sheep subspecies (Ovis nivicola lydekkeri) inhabiting various parts of the Verkhoyansk Mountain Range such as Kharaulakh Ridge, Orulgan Ridge, ridges of the Central Verkhoyansk, and Suntar-Khayata Ridge is presented. Fragment analysis using 17 microsatellite loci was carried out using the ABI 3131xl genetic analyzer. Significant heterozygote deficiency was detected in all investigated snow sheep populations. Differentiation of the studied groups in accordance to their geographical origin was revealed. [ABSTRACT FROM AUTHOR]

Abstract: Thousands of small populations are at increased risk of extinction because genetics and evolutionary biology are not well‐integrated into conservation planning–a major lost opportunity for effective actions. We propose that if the risk of outbreeding depression is low, the default should be to evaluate restoration of gene flow to small inbred populations of diploid outbreeding organisms that were isolated by human activities within the last 500 years, rather than inaction. We outline the elements of a scientific‐based genetic management policy for fragmented populations of plants and animals, and discuss the reasons why the current default policy is, inappropriately, inaction. [ABSTRACT FROM AUTHOR]

Abstract: Aim: Palaeoclimatic and palaeogeological events have been identified as two main factors that influence the genetic structuring of extant organisms. We studied a montane stream‐dwelling insect, Metrocoris sichuanensis, to explore the relative roles played by these two factors in population genetic connectivity. Location: Sichuan Basin, China. Methods: Mitochondrial (COI, COII, Cytb, 16S) and nuclear (EF‐1α, ITS1) markers were sequenced from 208 individuals. Suitable habitat shifts from the Last Glacial Maximum (LGM) to the present were predicted through fine‐tuned ecological niche modelling (ENM). Phylogenetic and phylogeographical analyses were conducted to reveal the population genetic structure. Intraspecific divergence and expansion times were estimated using beast. Finally, the least cost path (LCP) method coupled with migrate analysis was used to identify possible dispersal corridors and estimate the asymmetric gene flow. Results: Our ENM results suggested that population habitat connectivity did not change both in the LGM and current conditions. Whole haplotypes were separated into four highly supported clades/haplogroups that exhibited strong geographical structure. The splitting events between the four lineages likely date back to the Early Pleistocene. Bayesian skyline plot (BSP) indicated a moderate demographic growth from the LGM to the present. A putative dispersal corridor was detected along the Longmen Mountains thrust belt, with unidirectional gene flow from north to south. Main conclusion: Our findings support the geographical isolation of the genetic lineages and a deep early Pleistocene split in M. sichuanensis. Landscape connectivity analysis incorporating the genetic data and the ENM prediction revealed that population genetic connectivity was strongly associated with stable climatic habitats shaped by complex topography. The drainage system might have assisted the rapid movement of populations along the Longmen Mountains thrust belt. A strategy for researching the population genetic connectivity of narrow endemics, such as M. sichuanensis, in global biodiversity hotspots is proposed and discussed in this paper. [ABSTRACT FROM AUTHOR]

Abstract: Movement of species beyond their indigenous distribution can fundamentally alter the conservation status of the populations involved. If introductions are human‐facilitated, introduced species could be considered pests. Characterizing the colonization history of introduced species can therefore be critical to formulating the objectives and nature of wildlife management strategies. The black swan (Cygnus atratus) is native to Australia but is considered a reintroduced species in New Zealand, where the endemic population was reported extinct during the 19th century. After the reintroduction of a small number of individuals from Australia, the New Zealand population expanded unexpectedly rapidly, which was attributed to simultaneous waves of migration from Australia. An alternative, but hitherto unformalized, hypothesis is that local extant populations remained and admixed with introduced individuals. To contribute to our understanding of the reintroduction history of the species, we investigated dispersal patterns and demographic histories of seven populations from Australia and New Zealand, using population genetic inferences from a microsatellite dataset. Our results on genetic structure, dispersal rates, and demographic histories provide mixed evidence on the origin of New Zealand black swans. The hypothesis that reintroduced individuals mixed with remaining local individuals and that the subsequent dramatic population expansion may have been due to genetic rescue of the inbred indigenous population cannot be discarded and needs further investigation. [ABSTRACT FROM AUTHOR]

The Zagros and Alborz mountainous ridges can be regarded as one of the most interesting and known physical barriers responsible for the vicariance event. Based on the probable effect of Zagros Mountains on the rodent population vicariance, a research on Caucasian mole vole phylogeography, population genetic structure and diversity was designed along the mentioned mountainous areas. To this end, a total of 38 tissue samples were collected from the northern parts of the study area to the southern parts. Obtained mitochondrial cytb (1041 bp) sequences were used in this phylogenetic analysis. The phylogenetic analysis was based on the TRN+I evolutionary model and gaining Bayesian phylogenetic tree with maximum verification. By using median joining logic, the relationships between different acquired haplotypes were analyzed. It was shown that the Caucasian mole vole population had been disjointed (based on posterior probability of 1 and 100 bootstraps) along the Zagros mountainous ridges, especially in both geographical extremes located in the northern and southern parts of the mountainous ridges. Meanwhile from the 38 analyzed sequences, 17 haplotypes were obtained, of which 10 haplotypes were unique. The mutational steps between haplotypes were assessed by generating statistical parsimony haplotype networks, which yielded 36 mutational steps between the northern and southern populations. Based on neutrality tests and analyzing their power under sudden population expansions, it was found that this event happened around the northern and southern populations. Genetic distance of two percent between the northern and southern populations indicated the existence of local adaptations by these two groups, which can be regarded as evolutionary units. [ABSTRACT FROM AUTHOR]

Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as amodel system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system. [ABSTRACT FROM AUTHOR]

A genetic survey of Barbus cyri populations from two biogeographical endorheic basins (Caspian Sea and Urmia Lake) was carried out using a mitochondrial marker (partial D-loop) in order to ascertain intra- and inter-population genetic diversity, population demography and to address their genetic structure which is the key to conservation action planning. Analyses were conducted on sequences obtained from 68 individuals collected from 10 sampling sites, from two basins. By means of morphological characteristics all specimens collected from the Caspian Sea basin were ascribed to Barbus cyri. Genetic diversity values (h and π) of sampling groups were all different from 0 (in Babolrud River population) to 0.857 (in Kalibar River population). Population connectivity and colonization patterns of the studied area were inferred from an analysis of molecular variance distribution and evolutionary relationships among haplotypes. The results point to different levels of isolation among sampling groups due to ecological and anthropogenic factors and the effect of an artificial barrier on genetic variability and conservation status of the population. Finally, this study confirms the uncertainty associated with systematic classification of Barbus spp. based on morphological characters due to the phenotypic plasticity of the species. [ABSTRACT FROM AUTHOR]

Infections with equine herpesviruses ( EHVs) are widespread in equine populations worldwide. Whereas both EHV-1 and EHV-4 produce well-documented respiratory syndromes in equids, the contribution of EHV-2 and EHV-5 to disease of the respiratory tract is still enigmatic. This study describes the detection and genetic characterization of EHVs from equids with and without clinical respiratory disease. Virus-specific PCRs were used to detect EHV-1, -2, -4 and -5. From the total of 160 equids with respiratory disease, EHV-5 was detected at the highest prevalence (23.1%), followed by EHV-2 (20.0%), EHV-4 (8.1%) and EHV-1 (7.5%). Concurrent infections with EHV-2 and EHV-5 were recorded from nine (5.2%) diseased horses. Of the total of 111 clinically healthy equids, EHV-1 and EHV-4 were never detected whereas EHV-2 and EHV-5 were found in 8 (7.2%) and 18 (16.2%) horses, respectively. A significantly higher proportion of EHV-2-infected equids was observed in the respiratory disease group (32/160, 20.0%; P = 0.005) compared to those without disease (8/111; 7.2%). EHV-2-positive equids were three times more likely to display clinical signs of respiratory disease than EHV-2-negative equids ( OR 3.22, 95% CI: 1.42-7.28). For EHV-5, the observed difference was not statistically significant ( P = 0.166). The phylogenetic analysis of the gB gene revealed that the Ethiopian EHV-2 and EHV-5 strains had a remarkable genetic diversity, with a nucleotide sequence identity among each other that ranged from 94.0 to 99.4% and 95.1 to 100%, respectively. Moreover, the nucleotide sequence identity of EHV-2 and EHV-5 with isolates from other countries acquired from GenBank ranged from 92.9 to 99.1% and 95.1 to 99.5%, respectively. Our results suggest that besides EHV-1 and EHV-4, EHV-2 is likely to be an important contributor either to induce or predispose equids to respiratory disease. However, more work is needed to better understand the contribution of EHV-2 in the establishment of respiratory disease. [ABSTRACT FROM AUTHOR]

The short-haired Segugio Italiano and rough-haired Segugio Italiano are two breeds of Italian scenthound. The two breeds were subjected to divergent selection based on the type (long versus short) and pigmentation (fawn versus black & tan) of the hair, leading to the development of the two above-mentioned phenotypes. Microsatellites markers from 120 unrelated dogs were used to estimate the genetic variability within the two Segugio Italiano breeds and to assess if divergent selection for the two phenotypes has possibly led to the development of subpopulations distinguished by coat type and pigmentation. Finally, we also estimated the genetic distance between the two Segugio Italiano breeds and two other related breeds, Segugio Maremmano and Segugio dell'Appennino. The mean Fis, Fit and Fst values indicated a moderate level of inbreeding. In both breeds the mean observed heterozygosity was lower than the expected heterozygosity. The AMOVA, PCoA and STRUCTURE analyses showed lack of differentiation between the two breeds and the absence of substructuring in the population. Cavalli- Sforza chord distance, Nei's genetic distance and Reynolds-Weir Cockerham's genetic distance between the two Segugio Italiano breeds were low. Low genetic distances were also found between the Segugio Italiano and the others two related breeds indicating that there is no difference in terms of genetic distance among the three breeds despite the important phenotypic differences among them. This paper provides a basis to change the breeding guidelines of the four breeds in the light of these informations. [ABSTRACT FROM AUTHOR]

The flat-headed cat ( Prionailurus planiceps) is a wetland specialist, currently facing habitat loss on a serious scale due to massive destruction of lowland forests and wetlands in Southeast Asia. Despite its 'endangered' status in the IUCN Red List, there has virtually been no investigation on the population structure nor on the evolutionary history of the flat-headed cat. To fill this gap, we used full mitochondrial genome sequences, obtained from archival samples, covering the historical distribution of the flat-headed cat. Our data revealed a high genetic differentiation ( F = 0.81, P < 0.001) between mitochondrial lineages from Borneo and those from Thai-Malay Peninsula/Sumatra, a split that was dated to ~575 Kya. Such a significant differentiation clearly distinguishes the Bornean flat-headed cat population from all other populations and suggests that there should be a reassessment of the flat-headed cat's intraspecific taxonomy. However, morphological and nuclear data are required to corroborate our mtDNA results. Until such data become available, we recommend that for future conservation efforts and captive breeding programmes the two genetically distinct flat-headed cat populations are managed separately as two lineages to maintain the original genetic diversity of this endangered species. [ABSTRACT FROM AUTHOR]

Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effectiveex situandin situconservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation. In spite of these morphotypes, very little is known about the genetic characteristics of the three subspecies, hence no strict subspecies-based breeding plan for retaining the evolutionary characteristics in captive populations for subsequent re-introduction is available except for a few studies. We describe the genetic characteristics of these three subspecies using cytochrome b of the mtDNA genome (400 bp). The DNA sequence data indicated 11 variable sites within the three subspecies. Two paraphyletic clades, namely the Central India and Western-Eastern populations were found, whereas the Western and Eastern populations are monophyletic with a bootstrap value of 69% within the clade. We suggest the need of sorting these three subspecies using different molecular mtDNA markers in zoos for captive breeding purposes so as to retain the genetic diversity of the separate geographic clines and to use a subspecies-specific fixed-state nucleotide to assess the extent of poaching to avoid any population demography stochastically in India. [ABSTRACT FROM PUBLISHER]

Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels. [ABSTRACT FROM PUBLISHER]

It is believed that population structure of mountain horse breeds is preserved from any genetic introgression, because of their geographical isolation and specific semi-wild life style of husbandry. Till date there are no molecular data for the Balkan horses. In this study we try to give information about some autochthonous mountain horse breeds from Bulgaria. A total of 121 horses from three different mountain massifs are presented: Stara Planina (the Balkan mountain), the Rhodopes and Rila-Pirin massif were genotyped according to mitochondrial D-loop region. The results showed huge diversity of all known haplogroups with exception of C, F and R. West Eurasian haplogroups B, D, M and L were with the highest frequencies. Haplogroups A, J, I, O’P and Q were also observed with the highest frequencies, but not equally distributed among the three populations. Analyses of the horse breeds reveal preserved genetic profile of the Balkan and the Rhodopes mountains populations. In contrast, a Rila-Pirin breed unexpectedly showed mixed profile – a massive genetic introgression with an Asiatic-type haplogroups. A similar mixed Euro-Asiatic haplotype profile possessed the Carpathian mountain pony, although both populations are separated geographically and historically. The genetic pool of three Bulgarian mountain horse populations is highly heterogenic and because of that these breeds should be preserved. [ABSTRACT FROM PUBLISHER]