Tammy E. Steeves

Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population?” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise FST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.

The Isthmus of Panama: a major physical barrier to gene flow in a highly mobile pantropical seabird

To further test the hypothesis that the Isthmus of Panama is a major barrier to gene flow in pantropical seabirds, we applied phylogeographic methods to mitochondrial control sequence variation in masked booby (Sula dactylatra) populations on either side of the Isthmus of Panama and the southern tip of Africa. In accord with Steeves et al. (2003) , we found that all Caribbean masked boobies with the ‘secondary contact’ cytochrome b haplotype (m‐B) shared a control region haplotype (Sd_100), which grouped with Indian–Pacific haplotypes and not Caribbean–Atlantic haplotypes. In addition, Sd_100 was more closely related to control region haplotypes in the Indian Ocean than in the Pacific. We also found that the ‘secondary contact’ birds diverged more recently from extant populations in the Indian Ocean than in the Pacific. Thus, it appears that these masked boobies did not breach the Isthmus of Panama. Rather, birds likely dispersed around the southern tip of Africa during favourable oceanographic conditions in the Pleistocene.

A role for nonphysical barriers to gene flow in the diversification of a highly vagile seabird, the masked booby (Sula dactylatra)

To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low‐latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies (Sula dactylatra). In accord with previous studies, we found that Indo‐Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo‐Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher‐level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher‐level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo‐Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo‐Pacific populations. We estimate that Indo‐Pacific masked boobies experienced rapid population growth ∼180 000 years ago and that the majority of Indo‐Pacific and Atlantic populations diverged within the last ∼115 000 years. These combined data suggest that the predominant pattern between Indo‐Pacific and Atlantic populations is long‐term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.

Contemporary and historical separation of transequatorial migration between genetically distinct seabird populations

Pelagic seabirds are highly mobile, reducing the likelihood of allopatric speciation where disruption of gene flow between populations is caused by physically insurmountable, extrinsic barriers. Spatial segregation during the non-breeding season appears to provide an intrinsic barrier to gene flow among seabird populations that otherwise occupy nearby or overlapping regions during breeding, but how this is achieved remains unclear. Here we show that the two genetically distinct populations of Cooks petrel (Pterodroma cookii) exhibit transequatorial separation of non-breeding ranges at contemporary (ca. 2-3 yrs) and historical (ca. 100 yrs) time scales. Segregation during the non-breeding season per se appears as an unlikely barrier to gene flow. Instead we provide evidence that habitat specialization during the non-breeding season is associated with breeding asynchrony which, in conjunction with philopatry, restricts gene flow. Habitat specialization during breeding and non-breeding likely promotes evolutionary divergence between these two populations via local adaptation.

Comparative phylogeography of brown (Sula leucogaster) and red-footed boobies (S. sula): the influence of physical barriers and habitat preference on gene flow in pelagic seabirds.

To test the hypothesis that both physical and ecological barriers to gene flow drive population differentiation in tropical seabirds, we surveyed mitochondrial control region variation in 242 brown boobies (Sula leucogaster), which prefer inshore habitat, and 271 red-footed boobies (S. sula), which prefer pelagic habitat. To determine the relative influence of isolation and gene flow on population structure, we used both traditional methods and a recently developed statistical method based on coalescent theory and Bayesian inference (Isolation with Migration). We found that global population genetic structure was high in both species, and that female-mediated gene flow among ocean basins apparently has been restricted by major physical barriers including the Isthmus of Panama, and the periodic emergence of the Sunda and Sahul Shelves in Southeast Asia. In contrast, the evolutionary history of populations within ocean basins differed markedly between the two species. In brown boobies, we found high levels of population genetic differentiation and limited gene flow among colonies, even at spatial scales as small as 500km. Although red-footed booby colonies were also genetically differentiated within ocean basins, coalescent analyses indicated that populations have either diverged in the face of ongoing gene flow, or diverged without gene flow but recently made secondary contact. Regardless, gene flow among red-footed booby populations was higher than among brown booby populations. We suggest that these contrasting patterns of gene flow within ocean basins may be explained by the different habitat preferences of brown and red-footed boobies.

Genetic analyses reveal hybridization but no hybrid swarm in one of the world's rarest birds

Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī (Himantopus novaezelandiae), the risk associated with hybridization between this critically endangered endemic and its self-introduced congener, the pied stilt or poaka (Himantopus himantopus leucocephalus) is less clear. Here, we combine Bayesian admixture analyses of microsatellite data with mitochondrial DNA sequence data to assess the levels of hybridization and introgression between kakī and poaka. We show that birds classified as hybrids on the basis of adult plumage are indeed of hybrid origin and that hybridization between kakī and poaka is both extensive and bidirectional. Despite this, we found almost no evidence for introgression from poaka to kakī, thus negating the popular belief that kakī represent a hybrid swarm. To our knowledge, ours represents the first comprehensive study to document a lack of widespread introgression for a species at risk despite a recent history of extensive bidirectional human-induced hybridization. We attribute this rather surprising result, in part, to reduced reproductive success in female hybrids combined with a transient male-biased kakī sex ratio. To maximize the evolutionary potential of kakī, we use these data to recommend conservation management activities aimed to maintain the genetic integrity and to maximize the genetic diversity of this iconic rare bird.

Phylogeography of the New Zealand blue duck (Hymenolaimus malacorhynchos): implications for translocation and species recovery

Translocation of individuals among extant populations is an important tool in species conservation that allows managers to supplement dwindling populations and potentially alleviate the deleterious effects of inbreeding. Ideal translocation strategy should consider historical relationships among existing populations to avoid potential disruption of population subdivision and local adaptation. Here, we examine mitochondrial sequence variation in the endangered blue duck Hymenolaimus malacorhynchos, a New Zealand endemic riverine specialist, to facilitate informed decision making in future translocations. Behavioural observations suggest that blue duck dispersal is limited and may result in genetic structure within and between regional populations. We analysed 894 base pairs of mitochondrial control region in 78 adult blue ducks sampled from 11 river catchments across the species’ range (representing four regions in the North Island and three regions in the South Island) and found strong and significant genetic structure both within and among islands. These results, combined with a 2.0% sequence divergence between islands, indicates that North Island and South Island blue ducks should be treated as separate management units. The relationship between genetic differentiation and geographic distance for blue ducks on the South Island conformed to an “isolation by distance” pattern. Overall, we recommend that translocations of blue ducks should not be made between the North and the South Islands and those within each island should be restricted to neighbouring catchments.

Spending limited resources on de-extinction could lead to net biodiversity loss

There is contentious debate surrounding the merits of de-extinction as a biodiversity conservation tool. Here, we use extant analogues to predict conservation actions for potential de-extinction candidate species from New Zealand and the Australian state of New South Wales, and use a prioritization protocol to predict the impacts of reintroducing and maintaining populations of these species on conservation of extant threatened species. Even using the optimistic assumptions that resurrection of species is externally sponsored, and that actions for resurrected species can share costs with extant analogue species, public funding for conservation of resurrected species would lead to fewer extant species that could be conserved, suggesting net biodiversity loss. If full costs of establishment and maintenance for resurrected species populations were publicly funded, there could be substantial sacrifices in extant species conservation. If conservation of resurrected species populations could be fully externally sponsored, there could be benefits to extant threatened species. However, such benefits would be outweighed by opportunity costs, assuming such discretionary money could directly fund conservation of extant species. Potential sacrifices in conservation of extant species should be a crucial consideration in deciding whether to invest in de-extinction or focus our efforts on extant species.

Conservation and Losses of Non-Coding RNAs in Avian Genomes

Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous “losses” of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.

Maximising evolutionary potential in functional proxies for extinct species: a conservation genetic perspective on de‐extinction

Summary De-extinction sensu stricto is the resurrection of phenotypic traits once possessed by extinct species to create extant functional proxies. To realise the ecological benefit of de-extinction, self-sustaining (genetically viable) populations of functional proxies are required. It is often implied, yet rarely stated, that the genetic challenges associated with the survival and recovery of extant threatened species in an effort to conserve biodiversity are also relevant to the use of functional proxies of extinct species as a conversation tool. Here, we highlight the importance of prioritising evolutionary potential − the capacity to evolve (adapt) in response to environmental change − in populations of functional proxies. We use conservation genetic principles to describe impediments to the creation and maintenance of evolutionary potential as a series of potentially unavoidable genetic bottlenecks (pre-extinction, resurrection, captive, translocation). To give any successfully translocated populations of functional proxies the best chance to survive beyond the first few generations in the wild, we advocate the use of a holistic framework that includes the creation of sufficiently large, genetically diverse populations that harbour the ability to adapt to a changing environment. A lay summary is available for this article.