Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

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Phylogenies and Community Ecology

Whether inbreeding affects the demography and persistence of natural populations has been questioned. However, new pedigree data from field populations and molecular and analytical tools for tracing patterns of relationship and inbreeding have now enhanced our ability to detect inbreeding depression within and among wild populations. This work reveals that levels of inbreeding depression vary across taxa, populations and environments, but are usually substantial enough to affect both individual and population performance. Data from bird and mammal populations suggest that inbreeding depression often significantly affects birth weight, survival, reproduction and resistance to disease, predation and environmental stress. Plant studies, based mostly on comparing populations that differ in size or levels of genetic variation, also reveal significant inbreeding effects on seed set, germination, survival and resistance to stress. Data from butterflies, birds and plants demonstrate that populations with reduced genetic diversity often experience reduced growth and increased extinction rates. Crosses between such populations often result in heterosis. Such a genetic rescue effect might reflect the masking of fixed deleterious mutations. Thus, it might be necessary to retain gene flow among increasingly fragmented habitat patches to sustain populations that are sensitive to inbreeding.

Inbreeding effects in wild populations.

Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.

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The global diversity of birds in space and time

A DNA test to sex most birds.

Landscape Features Fail to Explain Spatial Genetic Structure in White-Tailed Deer Across Ohio, USA

Assessing the environmental factors that influence the ability of a threatened species to move through the landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the Eastern Massasauga Rattlesnake (Sistrurus catenatus). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity is impacted by both contemporary landcover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and Least Cost Paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for S. catenatus movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmentated landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.

Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics.

Ambystoma salamanders are amphibians that due to limited dispersal abilities and reliance on wetlands for breeding are susceptible to population declines and local extinctions (Blaustein et al. 2011). Species identification within Ambystoma is especially difficult due to the presence of unisexual Ambystoma that consist of multiple all-female lineages in which clones can have between two and five nuclear genomes from up to five other Ambystoma species (Bogart et al. 2007). The majority of these unisexual Ambystoma are composed of nuclear genomes from two species, A. laterale (Blue Spotted Salamander) and A. jeffersonianum (Jefferson Salamander). We developed species-specific microsatellite markers for these two species as a tool for the identification and investigation of the genetic interactions between sexual and unisexual groups in areas where either sexual species is endangered or of special conservation concern (Ohio, Indiana, and Ontario).

Development of 31 new microsatellite loci for two mole salamanders (Ambystoma laterale and A. jeffersonianum)

Venom is a hallmark example of animal evolution: the capacity to make and use toxins has arisen via natural selection multiple times in animals as diverse as corals, snails, spiders, snakes, and mammals (Casewell et al. 2013). This diversity within the animal tree of life is mirrored by diversity at the molecular and genetic level, as the proteins that make up venoms and the genes that specify these proteins evolve rapidly to fill diverse functional roles (Sunagar et al. 2016). Because of their remarkable molecular diversity, venoms are key, albeit challenging, resource for pharmacological discovery that contribute to the development of drugs that act as anti-tumor agents, heart stimulants, and therapies for neurological diseases (Harvey 2014). Venom biology is a multidimensional field, spanning the molecules and genes of the phenotype to the ecological consequences of its use (Calvete 2013). Those dimensions are integrated in the organisms that make and use the venom. Although there have been previous symposia and working groups devoted to venom, these have focused on either a single organismal lineage (e.g., King 2004; Kem and Turk 2009) or limited methodological approaches (e.g., Escoubas 2006; Calvete 2012). This symposium aimed to span the lineages and organizational levels at which venom is being studied and to develop links between these levels and across these lineages. All venoms are similar in being complex cocktails of proteins and other bioactive compounds that are injected by the manufacturing animal into another animal (Casewell et al. 2013). Even when venom is not homologous in a broad evolutionary sense, the genes that are recruited into venom may belong to the same gene families. Similarities in molecular targets and the need for functional redundancy for neofunctionalizing genes may limit the pool of possible gene families from which venom genes can be recruited (Fry et al. 2009). However, as Rodrı́guez de la Vega points out in his symposium contribution, because toxins may be recruited convergently from within the same large gene family, it is especially important to consider genes that encode non-toxin proteins or that are nonfunctional so as not to misinterpret the level of shared evolutionary history (Rodrı́guez de la Vega and Giraud 2016). This caution argues against exclusive or primary reliance on databases of genes and proteins linked to venom (e.g., ConoServer: Kaas et al. 2011; ToxProt: Jungo et al. 2012) as the source of genes and proteins for comparison and underscores the importance of genomic (rather than transcriptomic) approaches to understanding the molecular origin of venom (Reyes-Velasco et al. 2015). Although these databases are an important resource for detecting and interpreting the genes that contribute to venoms, for contextualizing the genes that encode venoms, coding genes without venom function and pseudogenes are likely as important as genes with known function in venom. The biochemical diversity of venoms poses a compelling system in which to understand the genetic and molecular origin of diversity and the ecological and evolutionary impact of this diversity (Sunagar et al. 2016). This is best understood for snakes and other lineages which have been more completely studied because they have a direct impact on human health. Nonetheless, for even these well Integrative and Comparative Biology

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Integrating Perspectives on Animal Venom Diversity: An Introduction to the Symposium.

Quantifying genetic introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what factors drive the longevity of putatively asexual groups. However, the presence of multiple distinct subgenomes within a single lineage provides a significant logistical challenge to evaluating the origin of genetic variation in most polyploids. Here, we capitalize on three recent innovations--variation generated from ultraconserved elements (UCEs), bioinformatic techniques for assessing variation in polyploids, and model-based methods for evaluating historical gene flow--to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. We first analyzed variation from more than a thousand UCEs using a reference mapping method developed for polyploids to infer subgenome specific patterns of variation in the all-female lineage. We then used PHRAPL to choose between sets of historical models that reflected different patterns of introgression and divergence between the genomes of the parental species and the same genomes found within the polyploids. Our analyses support a scenario in which the genomes sampled in unisexuals salamanders were present in the lineage ~3.4 million years ago, followed by an extended period of divergence from their parental species. Recent secondary introgression has occurred at different times between each sexual species and their representative genomes within the unisexuals during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage has been the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have also undergone long periods of divergence without introgression. Unlike other unisexual, sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could reveal the scenarios in which the influx of novel genomic material is favored and potentially explain why these salamanders are among the oldest described unisexual animals.

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H. Lisle Gibbs

Papers

Landscape Features Fail to Explain Spatial Genetic Structure in White-Tailed Deer Across Ohio, USA

Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics.

Development of 31 new microsatellite loci for two mole salamanders (Ambystoma laterale and A. jeffersonianum)

Integrating Perspectives on Animal Venom Diversity: An Introduction to the Symposium.

Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species