Anna B. Sellas

A phylogenomic analysis of turtles

Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses.

CHARACTERIZING SOURCE–SINK DYNAMICS WITH GENETIC PARENTAGE ASSIGNMENTS

Source-sink dynamics have been suggested to characterize the population structure of many species, but the prevalence of source-sink systems in nature is uncertain because of inherent challenges in estimating migration rates among populations. Migration rates are often difficult to estimate directly with demographic methods, and indirect genetic methods are subject to a variety of assumptions that are difficult to meet or to apply to evolutionary timescales. Furthermore, such methods cannot be rigorously applied to high-gene-flow species. Here, we employ genetic parentage assignments in conjunction with demographic simulations to infer the level of immigration into a putative sink population. We use individual-based demographic models to estimate expected distributions of parent-offspring dyads under competing sink and closed-population models. By comparing the actual number of parent-offspring dyads (identified from multilocus genetic profiles) in a random sample of individuals taken from a population to expectations under these two contrasting demographic models, it is possible to estimate the rate of immigration and test hypotheses related to the role of immigration on population processes on an ecological timescale. The difference in the expected number of parent-offspring dyads between the two population models was greatest when immigration into the sink population was high, indicating that unlike traditional population genetic inference models, the highest degree of statistical power is achieved for the approach presented here when migration rates are high. We used the proposed genetic parentage approach to demonstrate that a threatened population of Marbled Murrelets (Braclhyrarmphus marmotus) appears to be supplemented by a low level of immigration (approximately 2-6% annually) from other populations.

Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation

The dispersal of individuals among fragmented populations is generally thought to prevent genetic and demographic isolation, and ultimately reduce extinction risk. In this study, we show that a century of reduction in coastal old-growth forests, as well as a number of other environmental factors, has probably resulted in the genetic divergence of marbled murrelets (Brachyramphus marmoratus) in central California, despite the fact that 7 per cent of modern-sampled murrelets in this population were classified as migrants using genetic assignment tests. Genetic differentiation appears to persist because individuals dispersing from northern populations contributed relatively few young to the central California population, as indicated by the fact that migrants were much less likely to be members of parent–offspring pairs than residents (10.5% versus 45.4%). Moreover, a recent 1.4 per cent annual increase in the proportion of migrants in central California, without appreciable reproduction, may have masked an underlying decline in the resident population without resulting in demographic rescue. Our results emphasize the need to understand the behaviour of migrants and the extent to which they contribute offspring in order to determine whether dispersal results in gene flow and prevents declines in resident populations.

Isolation and characterization of polymorphic microsatellite markers from the spotted eagle ray (Aetobatus narinari)

Ten polymorphic microsatellites were isolated from the spotted eagle ray using an enrichment protocol. Primers were designed and tested on 30 individual samples collected in eastern Gulf of Mexico waters off Sarasota, FL. The number of alleles for these loci ranged from 2 to 19 and observed heterozygosities ranged from 0.345 to 0.966. All loci conformed to Hardy–Weinberg and linkage equilibrium. These markers are the first published microsatellites from A. narinari and will be valuable to studies investigating the population structure and conservation genetics of this near threatened species.

Population Structure and Seasonal Migration of the Spotted Eagle Ray, Aetobatus narinari

Few studies have reported on the fine-scale population genetics of batoid species in the Atlantic basin. Here, we investigate the genetic diversity and population structure of the spotted eagle ray, Aetobatus narinari, sampled in the northeastern and southwestern parts of the Gulf of Mexico and in the northwestern Caribbean Sea. Samples were collected from 286 individuals sampled across 3 geographic localities. Estimates of divergence based on the mitochondrial cytochrome b gene and 10 nuclear microsatellite loci reveal weak but significant genetic structure among A. narinari populations in this region. Analysis of molecular variance estimates based on both marker types indicate significant differentiation between Florida and Mexico populations, while comparisons with Cuba suggest high levels of gene flow with rays from both Mexico and Florida. Conflicting results were found from the different marker types when sexes were analyzed separately underscoring the importance of applying multiple marker types when making inferences about population structure and sex-biased dispersal. Results from Bayesian clustering analyses suggest rays may be migrating south out of the Gulf of Mexico and into the northwestern Caribbean Sea. Given the impacts of fisheries on this species, coupled with the lack of population genetic data available, these findings offer valuable information to aid with conservation management strategies.

Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

Abstract Laboratory techniques for high‐throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site‐associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site‐associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.

A new species of Hemidactylus (Squamata: Gekkonidae) from Príncipe Island, Gulf of Guinea, West Africa with comments on the African-Atlantic clade of Hemidactylus geckos

Abstract The remote oceanic Gulf of Guinea islands of São Tomé and Príncipe are home to a highly endemic herpetofauna, which has become the focus of modern, on-going scientific analysis only during the past decade. Until now, the endemic Hemidactylus greeffi Bocage 1886 (Greeffs giant gecko) has been considered to occur on both islands. Herein, we employ both new and previously published molecular data, along with differences in morphological characters, to demonstrate that the Príncipe populations are a full species distinct from H. greeffi. We describe the new species and restrict the range of H. greeffi to the island of São Tomé. The original unnumbered holotype of H. greeffii held in the Museu Bocage was destroyed in Lisbon and we have been unable to determine the collection provenance of unnumbered material treated by subsequent authors. We therefore designate a neotype for H. greeffi from California Academy of Science collections and provide morphological information on that species additional to that of earlier workers, based upon 14 specimens collected in various localities on São Tomé during the past decade.

PERMANENT GENETIC RESOURCES: Isolation and characterization of 10 tetranucleotide microsatellite loci in an enigmatic East African bird, the spot‐throat (Modulatrix stictigula)

We describe the isolation of 10 tetranucleotide microsatellites from the spot‐throat using an enrichment protocol. All loci were highly variable with the number of alleles ranging from six to 20 and observed heterozygosity ranging from 0.410 to 0.940. Although all loci were in Hardy–Weinberg equilibrium, locus Mst95 showed significant homozygote excess in both surveyed populations, possibly a consequence of the presence of null alleles at this locus. These loci will be used to determine the extent to which spot‐throat populations are isolated in order to help set conservation priorities for this ancient African lineage.

Isolation and characterization of 10 tetranucleotide microsatellite loci from the yellow-streaked greenbul (Phyllastrephus flavostriatus) and cross-species amplification in four closely related taxa

We describe the isolation of 10 tetranucleotide microsatellite loci from the yellow‐streaked greenbul using an enrichment protocol. All loci were highly variable with the number of alleles ranging from 8 to 13, and observed heterozygosity ranging from 0.652 to 0.870. All loci were in Hardy–Weinberg equilibrium; however, loci Pfl12 and Pfl54 showed significant linkage disequilibrium. All 10 loci successfully amplified and were polymorphic in at least one of four related Phyllastrephus species. These loci should prove to be widely applicable to studies of phylogeography, hybridization and paternity in African greenbuls.

Isolation and characterization of microsatellite markers for identifying hybridization and genetic pollution associated with red-eared slider turtles (Trachemys scripta elegans)

Fourteen microsatellite markers were isolated and characterized from a microsatellite enriched genomic library obtained for the invasive red-eared slider turtle Trachemys scripta elegans (TSE). All but one locus conformed to Hardy–Weinberg equilibrium and none displayed linkage disequilibrium. The number of alleles ranged from 5 to 17 with observed heterozygosity values ranging from 0.26 to 0.96 for 23 individuals collected from its native range in the Mississippi River drainage. These markers will be useful in characterizing TSE populations and invaded populations of other Trachemys and could aid in the development of conservation management policies for invasive TSE.