Background
DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.

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Identifying Canadian Freshwater Fishes through DNA Barcodes

The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats. Citation: Aplin KP, Suzuki H, Chinen AA, Chesser RT, ten Have J, et al. (2011) Multiple Geographic Origins of Commensalism and Complex Dispersal History of

https://repository.up.ac.za/bitstream/handle/2263/17665/Aplin_Multiple(2011).pdf;sequence=1

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

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases The region faces growing economical development that affects habitats, biodiversity and health Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within Berylmys and Rattus genera, where future taxonomic studies should be directed Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences

https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers17-09/010049660.pdf

Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

Recent and rapid radiations provide rich material to examine the factors that drive speciation. Most recent and rapid radiations that have been well-characterized involve species that exhibit overt ecomorphological differences associated with clear partitioning of ecological niches in sympatry. The most diverse genus of rodents, Rattus (66 species), evolved fairly recently, but without overt ecomorphological divergence among species. We used multilocus molecular phylogenetic data and five fossil calibrations to estimate the tempo of diversification in Rattus, and their radiation on Australia and New Guinea (Sahul, 24 species). Based on our analyses, the genus Rattus originated at a date centered on the Pliocene-Pleistocene boundary (1.84-3.17 Ma) with a subsequent colonization of Sahul in the middle Pleistocene (0.85-1.28 Ma). Given these dates, the per lineage diversification rates in Rattus and Sahulian Rattus are among the highest reported for vertebrates (1.1-1.9 and 1.6-3.0 species per lineage per million years, respectively). Despite their rapid diversification, Rattus display little ecomorphological divergence among species and do not fit clearly into current models of adaptive radiations. Lineage through time plots and ancestral state reconstruction of ecological characters suggest that diversification of Sahulian Rattus was most rapid early on as they expanded into novel ecological conditions. However, rapid lineage accumulation occurred even when morphological disparity within lineages was low suggesting that future studies consider other phenotypes in the diversification of Rattus.

Recent and rapid speciation with limited morphological disparity in the genus Rattus.

Aim To describe the phylogeographic patterns of the black rat, Rattus rattus, from islands in the western Indian Ocean where the species has been introduced (Madagascar and the neighbouring islands of Reunion, Mayotte and Grande Comore), in comparison with the postulated source area (India). Location Western Indian Ocean: India, Arabian Peninsula, East Africa and the islands of Madagascar, Reunion, Grande Comore and Mayotte. Methods Mitochondrial DNA (cytochrome b, tRNA and D-loop, 1762 bp) was sequenced for 71 individuals from 11 countries in the western Indian Ocean. A partial D-loop (419 bp) was also sequenced for eight populations from Madagascar (97 individuals), which were analysed in addition to six previously published populations from southern Madagascar. Results Haplotypes from India and the Arabian Peninsula occupied a basal position in the phylogenetic tree, whereas those from islands were distributed in different monophyletic clusters: Madagascar grouped with Mayotte, while Reunion and Grand Comore were present in two other separate groups. The only exception was one individual from Madagascar (out of 190) carrying a haplotype that clustered with those from Reunion and South Africa. 'Isolation with migration' simulations favoured a model with no recurrent migration between Oman and Madagascar. Mismatch distribution analyses dated the expansion of Malagasy populations on a time-scale compatible with human colonization history. Higher haplotype diversity and older expansion times were found on the east coast of Madagascar compared with the central highlands. Main conclusions Phylogeographic patterns supported the hypothesis of human-mediated colonization of R. rattus from source populations in either the native area (India) or anciently colonized regions (the Arabian Peninsula) to islands of the western Indian Ocean. Despite their proximity, each island has a distinct colonization history. Independent colonization events may have occurred simultaneously in Madagascar and Grande Comore, whereas Mayotte would have been colonized from Madagascar. Reunion was colonized independently, presumably from Europe. Malagasy populations may have originated from a single successful colonization event, followed by rapid expansion, first in coastal zones and then in the central highlands. The congruence of the observed phylogeographic pattern with human colonization events and pathways supports the potential relevance of the black rat in tracing human history.

Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar

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.

Identifying Rattus species using mitochondrial DNA.

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.

Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species.

Presented here are the most recent results of our studies of Rattus exulans, one of the main commensal animals transported across the Pacific by Lapita peoples and their descendants. We sampled several locations in Near Oceania to determine distribution of R. exulans mitochondrial DNA (mtDNA) haplotypes in the region. We also obtained data regarding distribution of other introduced Rattus species to several islands in the Bismarck Archipelago. Our results suggest that there were multiple introductions of R. exulans to the region, which may suggest a more complex history for Lapita populations in Near Oceania.

https://bioone.org/journals/pacific-science/volume-63/issue-4/049.063.0402/On-the-Rat-Trail-in-Near-Oceania--Applying-the/10.2984/049.063.0402.pdf

On the Rat Trail in Near Oceania: Applying the Commensal Model to the Question of the Lapita Colonization

Norway rats are a globally distributed invasive species, which have colonized many islands around the world, including in the South Atlantic Ocean. We investigated the phylogeography of Norway rats across the South Atlantic Ocean and bordering continental countries. We identified haplotypes from 517 bp of the hypervariable region I of the mitochondrial D-loop and constructed a Bayesian consensus tree and median-joining network incorporating all other publicly available haplotypes via an alignment of 364 bp. Three Norway rat haplotypes are present across the islands of the South Atlantic Ocean, including multiple haplotypes separated by geographic barriers within island groups. All three haplotypes have been previously recorded from European countries. Our results support the hypothesis of rapid Norway rat colonization of South Atlantic Ocean islands by sea-faring European nations from multiple European ports of origin. This seems to have been the predominant pathway for repeated Norway rat invasions of islands, even within the same archipelago, rather than within-island dispersal across geographic barriers.

https://www.mdpi.com/1424-2818/8/4/32/pdf

Phylogeography of Rattus norvegicus in the South Atlantic Ocean

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.

Melanie Hingston

Papers

Identifying Rattus species using mitochondrial DNA.

Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species.

On the Rat Trail in Near Oceania: Applying the Commensal Model to the Question of the Lapita Colonization

Phylogeography of Rattus norvegicus in the South Atlantic Ocean

The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi.