An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.

http://webpages.icav.up.pt/PTDC/BIA-BEC/099915/2008/4.Hewitt%202004%20PhilTransRSocLondB.pdf

Genetic consequences of climatic oscillations in the Quaternary.

Phylogenetic trees in insects are frequently dated by applying a ‘‘standard’’ mitochondrial DNA (mtDNA) clock estimated at 2.3% My � 1 , but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east–west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9–12 Mya. Based on these ‘‘known’’ dates, a divergence rate of 3.54% My � 1 for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineagespecific differences in rates when comparing data from various sources.

/pdf/revisiting-the-insect-mitochondrial-molecular-clock-the-mid-20mxotjk2v.pdf

Revisiting the Insect Mitochondrial Molecular Clock: The Mid-Aegean Trench Calibration

The evolutionary biology of the threespine stickleback

List of figures. List of tables. Preface. Acknowledgements. 1 The breadth of forensic entomology. 1.1 History of forensic entomology. 1.2 Indicators of time of death. 1.3 Stages of decomposition of a body. 1.4 Indicators of physical abuse. 1.5 Insect larvae: a resource for investigating drug consumption. 1.6 Insect contamination of food. 1.7 Further reading. 2 Identifying flies that are important in forensic entomology. 2.1 What is a fly and how do I spot one? 2.2 Forensically important families of flies. 2.3 DNA identification of forensically important fly species. 2.4 Further reading. 3 Identifying beetles that are important in forensic entomology. 3.1 What do beetles look like? 3.2 Features used in identifying forensically important beetle families. 3.3 Identification of beetle families using DNA. 3.4 Further reading. 4 The life cycles of flies and beetles. 4.1 The life stages of the fly. 4.2 The life stages of the beetle. 4.3 The influence of the environment on specific insect species. 4.4 Succession of insect species on the corpse and its role in post mortem estimation. 4.5 Review technique: preparing slides of larval spiracles or mouthparts - preparation of whole slide mounts. 4.6 Further reading. 5 Sampling at the crime scene. 5.1 Entomological equipment needed to sample from a corpse. 5.2 The sampling strategy for eggs. 5.3 Catching adult flying insects at the crime scene. 5.4 Catching adult crawling insects at the crime scene. 5.5 Obtaining meteorological data at the crime scene. 5.6 Review technique: investigating the influence of larval location. 5.7 Further reading. 6 Breeding entomological specimens from the crime scene. 6.1 Returning to the laboratory with the entomological evidence. 6.2 Fly-rearing conditions in the laboratory. 6.3 Conditions for successful rearing to the adult (imago) fly stage. 6.4 Beetle rearing in the laboratory. 6.5 Dietary requirements of insects reared in the laboratory. 6.6 Review technique: preserving and mounting insect specimens. 6.7 Further reading. 7 Calculating the post mortem interval. 7.1 Working out the base temperature. 7.2 Accumulated degree data. 7.3 Calculation of accumulated degree hours (or days) from crime scene data. 7.4 Sources of error. 7.5 Use of larval growth in length to determine post mortem interval (isomegalen and isomorphen diagrams). 7.6 Calculating post mortem interval using succession. 7.7 Review technique: interpretation of data from a crime scene case study. 7.8 Further reading. 8 Ecology of forensically important flies. 8.1 Ecological features of bluebottles (Calliphoridae). 8.2 Greenbottles - Lucilia spp. 8.3 Ecological associations with living organisms. 8.4 Further reading. 9 Ecology of selected forensically important beetles. 9.1 Categories of feeding relationship on a corpse. 9.2 Ecology of carrion beetles (Silphidae). 9.3 Ecology of skin, hide and larder beetles (Dermestidae). 9.4 Ecology of clown beetles (Histeridae). 9.5 Ecology of checkered or bone beetles (Cleridae). 9.6 Ecology of rove beetles (Staphylinidae). 9.7 Ecology of dung beetles (Scarabaeidae). 9.8 Ecology of trogid beetles (Trogidae). 9.9 Ecology of ground beetles (Carabidae). 9.10 Review technique: determination of succession and PMI. 9.11 Further reading. 10 The forensic entomologist in court. 10.1 The Statement of Witness. 10.2 Council for the Registration of Forensic Practitioners. 10.3 Communicating entomological facts in court. 10.4 Physical evidence: its continuity and integrity. 10.5 Review technique: writing a Statement of Witness using the post mortem calculations determined from details given in Chapter 7. 10.6 Further reading. 11 The role of professional associations for forensic entomologists. 11.1 Professional organizations. 11.2 Forensic entomology protocols. 11.3 Areas for future research. 11.4 Further reading. Glossary. References. Appendices. Appendix 1: Form for forensic entomology questions to be asked at the crime scene. Appendix 2: Answers to the calculation of the post mortem interval for the body at the Pleasure Gardens, Wingsea. Appendix 3: UK list of Calliphoridae (2006). Appendix 4: UK checklists for Coleoptera. Appendix 5: List of relevant UK legal acts and orders. Appendix 6: Selected sources of entomological equipment. Appendix 7: Legal information relevant to giving testimony as a forensic entomologist in the USA. Index.

Forensic Entomology: An Introduction

Approximately 20,000 years ago the last glacial maximum (LGM) radically altered the distributions of many Northern Hemisphere terrestrial organisms. Fewer studies describing the biogeographic responses of marine species to the LGM have been conducted, but existing genetic data from coastal marine species indicate that fewer taxa show clear signatures of post-LGM recolonization. We have assembled a mitochondrial DNA (mtDNA) data set for 14 co-distributed northeastern Pacific rocky-shore species from four phyla by combining new sequences from ten species with previously published sequences from eight species. Nuclear sequences from four species were retrieved from GenBank, plus we gathered new elongation factor 1-alpha sequences from the barnacle Balanus glandula. Results from demographic analyses of mtDNA for five (36%) species (Evasterias troschelii, Pisaster ochraceus, Littorina sitkana, L. scutulata, Xiphister mucosus) were consistent with large population expansions occurring near the LGM, a pattern expected if these species recently recolonized the region. However, seven (50%) species (Mytilus trossulus, M. californianus, B. glandula, S. cariosus, Patiria miniata, Katharina tunicata, X. atropurpureus) exhibited histories consistent with long-term stability in effective population size, a pattern indicative of regional persistence during the LGM. Two species of Nucella with significant mtDNA genetic structure showed spatially variable demographic histories. Multilocus analyses for five species were largely consistent with mtDNA: the majority of multilocus interpopulation divergence times significantly exceeded the LGM. Our results indicate that the LGM did not extirpate the majority of species in the northeastern Pacific; instead, regional persistence during the LGM appears a common biogeographic history for rocky-shore organisms in this region.

/pdf/the-expansion-contraction-model-of-pleistocene-biogeography-g6wcc55ixw.pdf

The ‘Expansion–Contraction’ model of Pleistocene biogeography: rocky shores suffer a sea change?

Morphological differentiation in the ground beetles of the Nebria gregaria group, found on the Queen Charlotte Islands, has been used as support for the glacial refugium proposed for the northwest coast of North America. Two members of this species group, N. charlottae and N. louiseae, are restricted to cobble beaches in this archipelago. A third, N. haida, is found only in alpine regions of the archipelago and the adjacent mainland. The remaining two species of the gregaria group, N. lituyae and N. gregaria, show highly restricted distributions in the mountains of the Alaska panhandle and on the beaches of the Aleutian Islands, respectively. To determine the relationships of the five species, we conducted phylogenetic analyses on nucleotide sequence data obtained from five regions of the mito- chondrial DNA. In total, 1835 bp were analyzed. The results suggest that one species, N. lituyae, does not belong in the gregaria group, and that only seven mutations separated the two most divergent of the four remaining species. We also conducted random amplified polymorphic DNA fingerprinting analyses on genomic DNA extracted from the five species. Analyses of genetic diversity revealed a lack of molecular differentiation among the Queen Charlotte species, suggesting that these populations may be postglacial in origin and that together N. gregaria, N. charlottae, N. louiseae, and N. haida might represent local variations of a single species. These results are consistent with conclusions derived for the morphological and genetical differentiation among Gasterosteus populations in the ar- chipelago.

/pdf/rapid-evolution-in-the-nebria-gregaria-group-coleoptera-4d1s3f19g5.pdf

Rapid evolution in the Nebria gregaria group (Coleoptera: Carabidae) and the paleogeography of the Queen Charlotte Islands.

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Rapid evolution in the Nebria gregaria group (Coleoptera: Carabidae) and the paleogeography of the Queen Charlotte Islands.