So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action - 'Water for Life' - 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8% of the Earth's surface, yet this tiny fraction of global water supports at least 100000 species out of approximately 1.8 million - almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the 'Water for Life' decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as 'receivers' of land-use effluents, and the problems posed by endemism and thus non-substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and - in the case of migrating aquatic fauna - downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade-offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long-term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management - one that has been appropriately termed 'reconciliation ecology'.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/96AA265E3D88C95FB802E7A73CCB4332/S1464793105006950a.pdf/div-class-title-freshwater-biodiversity-importance-threats-status-and-conservation-challenges-div.pdf

Freshwater biodiversity: importance, threats, status and conservation challenges

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

The link between species invasions and the extinction of natives is widely accepted by scientists as well as conservationists, but available data supporting invasion as a cause of extinctions are, in many cases, anecdotal, speculative and based upon limited observation. We pose the question, are aliens generally responsible for widespread extinctions? Our goal is to prompt a more critical synthesis and evaluation of the available data, and to suggest ways to take a more scientific, evidence-based approach to understanding the impact of invasive species on extinctions. Greater clarity in our understanding of these patterns will help us to focus on the most effective ways to reduce or mitigate extinction threats from invasive species.

/pdf/are-invasive-species-a-major-cause-of-extinctions-5bi8w8turr.pdf

Are invasive species a major cause of extinctions

During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types.

/pdf/a-review-on-snp-and-other-types-of-molecular-markers-and-2ugrb11hbd.pdf

A review on SNP and other types of molecular markers and their use in animal genetics

Pearly mussels (Unionacea) are widespread, abundant, and important in freshwater ecosystems around the world. Catastrophic declines in pearly mussel populations in North America and other parts of the world have led to a flurry of research on mussel biology, ecology, and conservation. Recent research on mussel feeding, life history, spatial patterning, and declines has augmented, modified, or overturned long-held ideas about the ecology of these animals. Pearly mussel research has begun to benefit from and contribute to current ideas about suspension feeding, life-history theory, metapopulations, flow refuges, spatial patterning and its effects, and management of endangered species. At the same time, significant gaps in understanding and apparent paradoxes in pearly mussel ecology have been exposed. To conserve remaining mussel populations, scientists and managers must simultaneously and aggressively pursue both rigorous research and conservation actions.

/pdf/changing-perspectives-on-pearly-mussels-north-america-s-most-2ilbnkrueq.pdf

Changing Perspectives on Pearly Mussels, North America's Most Imperiled Animals

Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5-37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available.

Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation

Overharvest and habitat alteration have led toa collapse of most commercial Atlantic sturgeon(Acipenser oxyrinchus oxyrinchus)fisheries while pushing the species to rarityor extirpation in most of its historical range. A biologically sound conservation program forthis species requires knowledge of its geneticdiversity and of the evolutionary relationshipsamong geographic populations. To address theseresearch needs, six microsatellite loci wereisolated from A. o. oxyrinchus. Pedigreeanalysis suggested that all are inherited in acodominant Mendelian pattern. The six lociwere tested in ten additional sturgeon speciesfrom three genera and three apparent ploidylevels (4n, 8n, 16n). Approximately 70% ofsuccessful locus-species amplifications werepolymorphic. Polysomy was observed most oftenin 8n and 16n species. Genetic diversity andpopulation structure of A. o. oxyrinchuswere assayed using three polymorphic Aoxmarkers and four markers developed from lakesturgeon (A. fulvescens). A. o.oxyrinchus were sampled from the AltamahaRiver, Georgia, USA north to the St. LawrenceRiver, Quebec, Canada. Gulf sturgeon, A.o. desotoi, were sampled from the SuwanneeRiver, Florida, USA, to assess differentiationbetween the subspecies. Seventy-seven alleleswere observed to segregate into uniquemultilocus genotypes for each of the 392individuals assayed. Mean diversity wasgreatest in the Chesapeake Bay (9.7 alleles perlocus) and Delaware River (7.4 alleles perlocus) collections, and lowest in the St.Lawrence River (4.6 alleles per locus). Meanheterozygosity across seven loci ranged from44.3% (St. Lawrence River) to 62.6% (Altamaha River). Significant allelic heterogeneity wasobserved in 82% of pairwise comparisons aswell as a global test (p < 0.0001) for A.o. oxyrinchus collections. Genetic distancesuggests the presence of at least sixsubpopulations in A. o. oxyrinchus: St.Lawrence River, St. John River, Hudson River,Delaware River, Albemarle Sound, and AltamahaRiver. Genetic and geographic distances werepositively correlated (r = 0.57, p < 0.03) amongA. o. oxyrinchus, suggesting isolation bydistance and philopatry. Hierarchical genediversity analysis indicated significantgenetic population structure at every level. Maximum likelihood assignment tests correctlyassigned individual fish to collection with ahigh rate of success (mean = 87.5%); this andother lines of evidence indicated that theChesapeake Bay collection represents a mixedpopulation of sub-adult sturgeon from northernand southern Atlantic coast populations. Population structure was correlated with thatsuggested by earlier mitochondrial (mt) DNAanalyses. Significant diversity was observedbetween two Canadian populations from whichonly a single mtDNA haplotype has beenreported.

Microsatellite DNA variation in Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and cross-species amplification in the Acipenseridae

Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship, population structure, and mixed‐fishery analyses

A nucleotide sequence analysis of the first internal transcribed spacer region (ITS-1) between the 5.8S and 18S ribosomal DNA genes (640 bp) and cytochrome c oxidase subunit I (COI) of mitochondrial DNA (mtDNA) (576 bp) was conducted for the freshwater bivalve Lasmigona subviridis and three congeners to determine the utility of these regions in identifying phylogeographic and phylogenetic structure. Sequence analysis of the ITS-1 region indicated a zone of discontinuity in the genetic population structure between a group of L. subviridis populations inhabiting the Susquehanna and Potomac Rivers and more southern populations. Moreover, haplotype patterns resulting from variation in the COI region suggested an absence of gene exchange between tributaries within two different river drainages, as well as between adjacent rivers systems. The authors recommend that the northern and southern populations, which are reproductively isolated and constitute evolutionarily significant lineages, be managed as separate conservation units. Results from the COI region suggest that, in some cases, unionid relocations should be avoided between tributaries of the same drainage because these populations may have been reproductively isolated for thousands of generations. Therefore, unionid bivalves distributed among discontinuous habitats (e.g. Atlantic slope drainages) potentially should be considered evolutionarily distinct. The DNA sequence divergences observed in the nuclear and mtDNA regions among the Lasmigona species were congruent, although the level of divergence in the COI region was up to three times greater. The genus Lasmigona, as represented by the four species surveyed in this study, may not be monophyletic.

Tim L. King

Papers

Changing Perspectives on Pearly Mussels, North America's Most Imperiled Animals

Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation

Microsatellite DNA variation in Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and cross-species amplification in the Acipenseridae

Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship, population structure, and mixed‐fishery analyses

Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): conservation implications of range discontinuity