Over the past twenty years, several techniques from biochemical and molecular genetics, such as enzyme electrophoresis and isoelectric focusing, have been widely and successfully applied to the study of population differentiation and evolution. However, they have been less applicable to demographic problems such as assigning parentage to individuals within a population. This stems from a general weakness of data derived from enzyme loci: allele frequencies at polymorphic loci are sufficiently skewed that the majority of individuals are of one or two genotypes. Many enzyme systems can only be examined post mortem, so that the loci are of little use if the animals are to be studied in the wild. The search for new and more sensitive techniques for detecting genetic variation has continued, and recently a major discovery has come from molecular biology. Jeffreys et al. have reported the detection of a type of hypervariable 'minisatellite' DNA that is extraordinarily polymorphic in human populations. We have applied their technique to several bird species and particularly to a population of house sparrows (Passer domesticus) near Nottingham. We report here that one of the human minisatellite clones is a suitable probe for sparrow DNA and that it reveals variation as extensive as that found in man. These results suggest that analysis of minisatellite DNA will be a powerful tool in the study of demographic population genetics.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

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Microsatellites possess two major advantages over allozymes, RFLPs and minisatellites as a source of informative genetic markers. First, their amplification by PCR avoids the need for direct assaying of high quality DNA allowing the use of feathers and degraded material where appropriate, and secondly the resolution of PCR products on polyacrylamide gels clearly differentiates all alleles that differ in length. Hence microsatellites can be used to expand the scope and precision of population studies initiated with less sensitive marker systems (Queller et nl. 1993).We report here the isolation and characterization of microsatellite loci in the house sparrow for demographic and population genetic use. Both allozymes (Wetton et al. 1992) and multilocus DNA fingerprinting (Wetton et al. 1987; Wetton & Parkin 1991) have been used to determine the frequency of extra-pair fertilization in sparrows whilst the extra-pair sires have been identified by minisatellite single-locus profiling (Wetton ef al. 1995). Although capable of detecting all cases of incorrectly assigned paternity among sampled young, the surveys could take no account of the effect of differential mortality upon cuckolded broods as sampling was delayed until near fledging in order to obtain blood without harming the young. The study was also hampered by the quasi-continuous size distribution observed at minisatellite loci, which necessitated direct comparison of multilocus fingerprints on the same gel or wide error l i m i t s when matching single-locus profiles between gels. The problem is even more serious for inter-population studies as the standard methods of population genetics are rendered inappropriate by the extreme difficulty of estimating allele frequenaes at highly polymorphic minisatellite loci. These problems have been largely circumvented with microsatellites.House sparrow genomic libraries were established in DH5a (Gibco BRL) and XL-1 Blue MRF' (Stratagene) transformed with size fractionated (0.6-1 kb) MboI fragments *Corresponding author, Tel.: (0115) 9709399, Fax: (0115) 9709906, E-mail PDZJHW@pdnl .nott.ac.uk ligated into the BamHI site of pGEM-'/Zf(-) (Promega) and doubIy digested HaeIIIIAluI fragments (0.6-1 kb) in the SmaI site of pUCl8 (Pharmacia), respectively. One thousand recombinant clones from each library were transferred into individual wells of a miaotitre plate and replica plated onto nylon membranes in an ordered array (Armour et al. 1990). Colonies were screened with a cocktail of end-labelled oligonucleotides (CA),, (CT),, (CCAT), (GGGT), (GGAT), (GGGA), (GGAA), (AAAG), and (T'ITG),. Three positive clones from the first library and six from the second were sequenced, and primers were designed for the amplification of the repetitive region. Preliminary screening of 10 unrelated sparrows revealed four highly polymorphic loci which were chosen for further characterization. Two of the clones contain tailed dinucleotide tracts [Pdopl (G&(TGh and Pdop2 (TMGT), J, one a tetranucleotide repeat [Pdup.3 (TCCA),,], whilst the fou...

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Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for Saudi Arabia generally, and caution is needed when considering expatriate groups as representative of country of origin. Our study shows the importance of geographical and social structuring that may affect the utility of forensic databases and the interpretation of Y-STR profiles.

Illegal wildlife trade is gaining prominence as a threat to biodiversity, but addressing it remains challenging. To help inform proactive policy responses in the face of uncertainty, in 2018 we conducted a horizon scan of significant emerging issues. We built upon existing iterative horizon scanning methods, using an open and global participatory approach to evaluate and rank issues from a diverse range of sources. Prioritized issues related to three themes: developments in biological, information, and financial technologies; changing trends in demand and information; and socioeconomic, geopolitical shifts and influences. The issues covered areas ranging from changing demographic and economic factors to innovations in technology and communications that affect illegal wildlife trade markets globally; the top three issues related to China, illustrating its vital role in tackling emerging threats. This analysis can support national governments, international bodies, researchers, and nongovernmental organizations as they develop strategies for addressing the illegal wildlife trade.