In recent years, research has shown that geographical variation in mitochondrial DNA of commensal rats provides a strong signal of human dispersal and migration. However, interpretation of genetic variation is complicated by the presence of multiple species of Rattus especially in Island Southeast Asia, by the occurrence of some of these Rattus sp. as subfossils in archaeological and natural sites, and by the difficulty of osteological identification of these remains. Amplification of DNA from ancient sources usually yields only small fragments (∼200 bp). We assessed whether we could identify Rattus sp. reliably with DNA barcoding using cytochrome oxidase I (COI) sequences, or tree‐based methods using D‐loop, cytochrome b and COI sequences. Species forming well‐differentiated clades in a molecular phylogeny were accurately identified by both methods, even when we used short DNA fragments. Identification was less accurate for paraphyletic and polyphyletic species. We suggest that taxonomic revisions that recognize cryptic or polytypic species will lead to even greater accuracy of DNA‐based identification methods.

Aim  Description of the genetic differentiation of Rattus rattus populations in southern Madagascar. Reconstruction of the colonization pattern of R. rattus in southern Madagascar and of the origin of introduced R. rattus. Location  Southern Madagascar. Methods  We analysed the variation in the non‐coding hypervariable region 1 (HVR I) of the mitochondrial control region in 93 individuals from six different sampling sites. The origin of the introduced individuals was examined by comparing Malagasy R. rattus sequences to data available from outside Madagascar. Results  Thirteen distinct mtDNA control region haplotypes (H1–H13) were distinguished. Only 11 sites (2.6%) were variable within a 419‐bp sequence. Three haplotypes were shared between the sampling areas, though only one haplotype was ubiquitous accounting for 63.4% of all individuals. Population genetic differences (ΦST) between sampling sites ranged from 0.13 to 0.31. amova results showed that the majority of variation (86.1%) was assigned to diversity within populations. Except for two R. rattus sequences from India, all other outgroup samples (New York, Great Britain, France and French Polynesia) belonged to an identical haplotype. Main conclusions  The spatial distribution and frequency of haplotypes and associated phylogenetic analysis provisionally suggest the Tolagnaro harbour as the place of the founder population from which R. rattus spread into southern Madagascar. Given currently available samples, these populations are most closely related to rats from the Indian subcontinent. Corroboration of each of these hypotheses will require additional geographical sampling, particularly from northern Madagascar and Africa.

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region.

Next‐generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost‐effective identification of genome‐wide variation. Single nucleotide polymorphism (SNP) arrays, or “SNP chips”, enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction‐aided digest sequencing (RAD‐seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low‐coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD‐seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost‐effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.

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