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This chapter assesses the biogeography of chestnut-backed chickadees using microsatellite analysis, providing alternative scenarios for the glacial refugia and dispersal patterns that could explain the present distribution of distinct, genetic populations. This chapter also considers the potential for hybridization within the brown-capped chickadees to contribute to differentiation among disjunct populations within the chestnut-backed chickadees of northwestern Canada and Alaska. The factors influencing contemporary patterns of population structure in chestnut-backed chickadees are considered, including historical range expansion and geographic distribution, while potential barriers to dispersal are discussed. The patterns found in this western North American species are compared to those of other North American and Eurasian Parids. The population structure of chestnut-backed chickadees, and that of other Parids, appears to be complex and influenced by a variety of factors, most notably postglacial colonization and distribution. Many of the factors limiting dispersal in chestnut-backed chickadees seem to be common in other Parids. These include isolation of peripheral populations, and limited dispersal over large water barriers or other areas of unsuitable habitat.

The Late Quaternary palaeoecological record represents a source of baseline data for evidence-based conservation, by providing novel insights into how organisms and environments are likely to respond to the negative effects of future climate change. Palaeoecological data can reveal how individual taxa have responded in the past to specific climatic and environmental changes, and can suggest the kinds of processes that are likely to take place in the future at a broader ecological level. Conservation priority should be given to populations living in ‘long-term’ or ‘true’ geographic refugia where genetic diversity evolves. A lack of consideration of intraspecific-level extinction, increasingly recognised in the Quaternary record, has hampered interpretation of the causes of past species extinctions. Non-analogue ecological communities are commonly observed in the Quaternary record, suggesting that there will be a significant level of unpredictability in environmental responses to climatic change at the community level.

This chapter reviews evidence from research on the phylogenetics and phylogeography of Central American freshwater fishes, particularly in the Isthmus of Panama. It aims to address the question of the timing of the origins of the major taxonomic components of the fauna. It explains that the traditional interpretation of The Great American Biotic Interchange is inconsistent with the newly available phylogenetic and paleogeographic information on freshwater fishes and suggests that the prevailing view of a predominantly south-to-north faunal exchange starting about three million years ago that was the source of much of the current Central American ichthyofauna is an overly simplistic interpretation.

Molecular genetic tools are helping us to reconstruct the evolutionary history of juncos and thus to understand the factors, mechanisms and timing of their diversification. A new phylogeny based on sequence from the cytochrome c oxidase I gene and including all main junco groups confirms the recent diversification of dark-eyed juncos within the last 10,000 years, and reveals that lineages in isolated areas such as Baja California, Guadalupe Island and the highlands of Guatemala have been isolated for hundreds of thousands of years, yet they have differentiated relatively little in plumage color. We conclude that some phenotypic traits, such as eye color and several plumage color traits are labile and not phylogenetically informative, whereas others such as bill color or song characters are more consistent with lineage history. Long-term geographic isolation seems to be the main factor driving the divergence of Guatemala, Baird’s and Guadalupe juncos, whereas a role for selection must be invoked to explain the rapid divergence of continental dark-eyed junco taxa from yellow-eyed juncos. Based on currently available data and practical considerations, we propose that six species-level taxa be recognized within the genus.

This chapter provides a synthesis and evaluation of molecular techniques in the study of primate ecology, evolution, and conservation. It discusses how to obtain, preserve, and transport samples for genetic analysis; laboratory techniques for DNA extraction, genotyping, and sequencing; and data analyses relevant to research questions at the species- and population-level, including population genetics, molecular phylogenetics, and phylogeography. The chapter also highlights new and emerging approaches, including next-generation sequencing and landscape genetics. Discussed throughout is the relevance of these methods to various research questions related to primate conservation as well as ecology and evolution. In particular, molecular approaches allow research questions to not only address patterns, but also the ecological and evolutionary processes behind those patterns, enabling the conservation of natural populations that are capable of coping with continued environmental change.

The interstitial habitats along rivers and streams are generally small-pore SSHs, ones where the dissolution of bedrock plays little if any role. The best-studied and most ubiquitous of these habitats is the hyporheic, the underflow of rivers and streams. The hyporheic is an ecotone between surface and subsurface habitats, and is a filter in three ways—a photic filter, a mechanical filter, and a biochemical filter. Transfers occur in both directions, and a characteristic feature of the hyporheic is that there are series of upwellings of groundwater and downwellings of surface water. Oxygen concentrations are among the most critical parameters of the hyporheic and some species are only found in areas of low oxygen concentrations. Organic carbon is typically higher than in other SSHs, and particulate organic matter (POM), in addition to dissolved organic matter (DOM), may be an important organic carbon source. Little is known about large-scale patterns of species richness in spite of the possibility of quantitative, comparative sampling. At the local level, species richness can be quite high, typically with up to a hundred species and perhaps ten to twenty stygobionts. From a short-term ecological perspective, the hyporheos may serve as a refuge from flooding, from drying, and from competition and predation. Based on detailed studies of the phylogeography of the amphipod Niphargus rhenorhodanensis, Lefébure et al. (2007) concluded that subterranean dispersal of hyporheic species along river corridors did occur, but it was limited in extent, on the order of 200–300 km.

The Patagonian–Fuegian region comprises areas of Argentinean monte, Patagonian steppe and grasslands, and Valdivian temperate and Magellanic sub polar forests. Although the area was affected by the glacial cycles of the Neogene, glacial sheets were typically much more limited in South America than in northern continents. This chapter reviews the distributional, phylogenetic, phylogeographic, and population genetic information on the composition and historical biogeography of mammals in the region. Although many species are likely relatively recent colonizers of the region, distributional and phylogenetic data provide several examples of endemic species and others that likely resulted from local diversification. Phylogeographic analyses provide additional indications of differentiation within the region. Phylogeographic breaks divide species distributions by latitude rather than between major habitats. Population genetic analyses reveal several cases of demographic expansion, all of which can be assigned to the late Pleistocene (i.e., the last 500,000 years). However, very few of these can be attributed to events postdating the Last Glacial Maximum. The current mammalian fauna of Patagonia and Tierra del Fuego is the result of a complex mix of local fragmentation, differentiation, and colonization from lower latitudes.

The Amboseli population provides one of the best opportunities to understand how mating and dispersal behavior, long-term patterns of gene flow, and effective population size work together to structure genetic variation within and between populations. Amboseli has been relatively unaffected by the anthropogenic problems of poaching and habitat destruction, and much is known about the demography and behavior of the population over the duration of the project. This chapter first briefly reviews what is known about the genetic structure within populations, with a focus on the elephant population in the Amboseli ecosystem, and second, investigates how the genetic variation in Amboseli relates to the phylogeography of elephant populations on Kilimanjaro and the rest of the African continent.

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

Warning colour patterns in Heliconius show great diversity as well as convergence due to mimicry. This chapter considers the origins of such diversity. Heliconius have been proposed as an example of the ‘shifting balance’, an evolutionary model involving a balance between drift and selection. Although alternative mimicry patterns can move around the species range (Phase III), there is only weak evidence for genetic drift causing evolutionary novelty in wing patterns (Phase I). There is also weak evidence for the origin of novel patterns in Pleistocene forest refugia. Sequencing of the genes that control wing pattern diversity has revealed a surprising and complex history. Within-species disjunct populations with similar wing patterns show a common origin, suggesting a complex history of movement of patterning alleles across species ranges. Between species, convergent mimetic forms share alleles, likely due to adaptive introgression. Closely related species therefore evolve mimicry by sharing of alleles rather than independent convergence. These patterns contrast with phylogeographic and phylogenetic relationships inferred from the rest of the genome, and suggest caution in inferring the history of adaptive traits from ‘neutral’ molecular markers.

Colonization and speciation in subterranean environments can be conveniently divided into four stages. The first step is colonization of subsurface environments. There is a constant flux of colonists into most subterranean habitats. The second step is the success (or failure) of these colonizations. The third step is speciation. Under the Climate Relict Hypothesis (CRH) surface populations go extinct but under the Adaptive Shift Hypothesis (ASH) they do not necessarily do so, and speciation can be parapatric. There is strong evidence for the CRH among temperate zone fauna, and growing evidence for the ASH in tropical caves, especially lava tubes. The final step is possible further speciation as a result of subsurface dispersal. Detailed analysis of the evolutionary history of the isopod A. aquaticus in the Dinaric karst, diving beetles Paroster in a calcrete aquifer in Western Australia, and trogloxenic Leopoldamys neilli in Thailand reveal some of the complexities of species’ phylogeography.

The red panda is listed on the 2016 IUCN red list as Endangered. It is now distributed only in China, Myanmar, India, Bhutan and Nepal. Human activities such as poaching and large-scale deforestation have caused serious declines in this forest-dwelling species. Although its ecological research has made much progress in the past decades, only recently witnessed the population genetic research advances of this species. This chapter reviews the advances in wild red panda conservation genetics from non-invasive genetics, genetic diversity, phylogeographic structure, population genetic structure, demographic history, subspecies differentiation, to its conservation and management. It presents detailed estimates of genetic diversity, assesses the role of paleo-climate changes, human activities and landscape features in shaping the genetic structure and demographic history of red pandas, and discusses the implications of conservation genetics findings for effective genetic monitoring and conservation management.

How can genetics and genomics be used to understand the evolutionary history of organisms? This chapter focuses on such methods. First, the field of phylogenetics is introduced, as a way to visualize and quantify the evolutionary relationships among species. The chapter outlines how we go from aligning DNA sequence data to building gene trees and we argue that “tree-thinking” is fundamentally important for understanding evolution. The chapter also goes beyond phylogenetic trees to focus on phylogeography, i.e. the understanding of evolutionary relationships in a spatial context. More recently, the explosion of genomic data from ancient and modern human populations has made this an extremely exciting field which is transforming our understanding of our own evolutionary history. Before that, though, the chapter reviews how modern phylogenetics has arisen from historical efforts to classify life on Earth.

Present day genetic diversity within the Greater Cape Floristic Region (GCFR) is attributed to diversification during the Pliocene (5–2.5 Ma) and Pleistocene (2.5 Ma–20,000), due to the substantial phylogeographic structuring in many taxa examined, including plants, invertebrates, amphibians, reptiles, mammals, and birds. Diversification on this timescale is relatively recent, and the result is characteristically shallow genetic lineages, recently radiated species, and species complexes. Most phylogeographic structure is attributed to diversification events in the Late Miocene and Pliocene, often associated with recently diverged species which are usually reciprocally monophyletic but exhibit shallow divergences. More recent diversification events date to the Pleistocene, but these appear to be either divergence events among populations within species, or in some cases between species that are not reciprocally monophyletic and share ancestral polymorphisms. Discrete geographic boundaries among these clades are sometimes blurred, with alleles or haplotypes shared across some geographic regions or habitat types. Across the entire region, genetic diversity appears to be higher in the western GCFR, as compared to the east. This is possibly explained by the high stability of the region, and the associated potential for multiple refugia in the west. Regardless, the finer-scale patterns are not congruent among major groups, i.e. plants, invertebrates, amphibians, reptiles, mammals and birds, or within them, suggesting that there is no set of common environmental factors that can explain the phylogeographic patterns and cladogenesis in the GCFR. Instead, species presumably respond differentially depending on their habitat requirements, life history, and adaptive potential.

Crustacea display diverse life histories and occur in all marine habitats. This makes them particularly useful when thinking about how we can predict geographical distribution from life history and ecology. As would be expected from such diversity, crustaceans exhibit various population connectivity patterns, from panmictic, well-connected populations to small and isolated populations. Here we ask first what can be learned from exploring crustacean phylogeography and connectivity around well-understood vicariance events with known ages. We find that vicariance events are generally useful in calibrating molecular rates of evolution, but that there is substantial variation between taxa. This variation can be linked, on the one hand, to habitat differences (which determine when gene flow between populations actually ceased) and, on the other hand, to population size differences (which determine how fast genetic differences accumulate). In a few instances, populations must have diverged much earlier or later than the hypothesized vicariance event, providing evidence of earlier or later dispersal or more ancient separation. Second, we ask when comparative studies of multiple taxa show consistent results, predictable from their similar life history, and when not. For example, species that disperse little, such as brooding peracarids, have smaller, more isolated populations than species with planktonic larvae, such as decapods. Less consistent are the patterns across biogeographic breaks. While gene flow is clearly limited across such breaks in some species, other species do not seem to perceive them. This to-date-unexplained variation challenges our understanding of marine phylogeography.