Contemporary Genetic Diversity Research Articles

Phylogeography and potential glacial refugia of terrestrial gastropod Faustina faustina (Rossm\xe4ssler, 1835) (Gastropoda: Eupulmonata: Helicidae) inferred from molecular data and species distribution models

Faustina faustina is a conchologically highly diverse forest gastropod with several morphological forms. It is a Carpathian species, but it also occurs in northern isolated localities, where it was probably introduced. We performed the first phylogeographic analysis of 22 populations, based on three molecular markers: COI, ITS-2, and 28S rRNA. Genetic data were complemented by paleo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. We discovered high genetic variability of COI sequences with p-distances between haplotypes ranged from 0.2 to 18.1% (6.3–16.6% between clades). For nuclear markers, a haplotype distribution pattern was revealed. Species distribution models indicated a few potential refugia in the Carpathians, with the most climatically stable and largest areas in the Southern Carpathians. In some climate scenarios, putative microrefugia were also predicted in the Western and Eastern Carpathians, and in the Apuseni Mts. Our results suggest the glacial in situ survival of F. faustina and its Holocene expansion in the Sudetes. Although our genetic data as well as shell phenotypes showed considerable variation within and between studied populations, the molecular species delimitation approaches still imply only one single species. Our study contributes to the understanding of the impact of processes on shaping contemporary population genetic structure and diversity in low-dispersal, forest species.

Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning

Translocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.

Comparative analysis of the multivariate genetic architecture of morphological traits in three species of Gomphocerine grasshoppers.

Evolutionary change is the change in trait values across generations, and usually occurs in multidimensional trait space rather than along isolated traits. Genetic covariation influences the magnitude and direction of evolutionary change and can be statistically summarized by the additive genetic (co)variance matrix, G. While G can affect the response to selection, it is exposed to evolutionary change by selection and genetic drift, but the magnitude and speed of these changes are poorly understood. We use comparative G matrix analyses to assess evolution of the shape and orientation of G over longer timescales in three species of Gomphocerine grasshoppers. We estimate 10 × 10 G matrices for five morphological traits expressed in both sexes. We find low-to-moderate heritabilities (average 0.36), mostly large cross-sex correlations (average 0.54) and moderate between-trait correlations (average 0.34). G matrices differ significantly among species with wing length contributing most to these differences. Wing length is the trait that is most divergent among species, suggesting it has been under selection during species divergence. The more distantly related species, Pseudochorthippus parallelus, was the most different in the shape of G. Projection of contemporary genetic variation into the divergence space D illustrates that the major axis of genetic variation in Gomphocerippus rufus is aligned with divergence from Chorthippus biguttulus, while the major axis of genetic variation in neither of the species is aligned with the divergence between Pseudochorthippus parallelus and the other two species. Our results demonstrate significant differences in G matrices with a phylogenetic signal in the differentiation.

Navigating the southern seas with small fins: Genetic connectivity of seahorses (Hippocampus abdominalis) across the Tasman Sea

AbstractAimHistorical patterns of ocean circulation in the Southern Hemisphere have been well‐studied, but the effects of coastal oceanography on marine biogeography in this region remain poorly understood relative to northern latitudes. Our study investigates historical and contemporary patterns of migration and dispersal across the Tasman Sea.LocationCoastal regions of the Tasman Sea including southeastern Australia, Tasmania and New Zealand.TaxonHippocampus abdominalis, the pot‐bellied seahorse, one of the most broadly distributed seahorse species, and the only seahorse to have successfully colonized New Zealand from Australia across 2,000 km of open ocean.MethodsWe used a multilocus genetic dataset to measure population diversity and differentiation from seahorses across the full species range to investigate contemporary and historical demography, and to reconstruct colonization routes across the Tasman Sea.ResultsGenetic data indicate that seahorses colonized New Zealand from Australia during the previous interglacial‐glacial cycle (12,000–120,000 ybp), and have evolved in relative isolation since the initial establishment event. Contemporary effective population sizes in the newly colonized range are substantially larger than those inferred in Australia, and both appear to be reduced relative to ancestral levels. Australian seahorses are genetically diverse and show high levels of population connectivity, while the distribution of genetic variation in New Zealand suggests an initial colonization of the South Island following by northward migration. Importantly, despite clear evidence that New Zealand seahorses are descendent from Australian ancestors, patterns of contemporary genetic diversity are consistent with trans‐Tasman migration from New Zealand to Australia, suggesting that genetic variation accumulated in the newly colonized range may be contributing to the genetic diversity of Australian seahorses.Main conclusionsDespite a largely independent evolutionary trajectory of seahorses separated by the Tasman Sea, haplotype sharing between populations in Australia and New Zealand suggests that secondary genetic exchange is contributing to the contemporary phylogeography of the species. Patterns of genetic structure in H. abdominalis mirror those found in other rafting species, suggesting that adult dispersal via rafting has been an important vector of marine dispersal in this species.

Phylogeographic and evolutionary history analyses of the warty crab Eriphia verrucosa (Decapoda, Brachyura, Eriphiidae) unveil genetic imprints of a late Pleistocene vicariant event across the Gibraltar Strait, erased by postglacial expansion and admixture among refugial lineages

BackgroundThe Pleistocene cyclic sea-level fluctuations are thought to have markedly affected the distribution and genetic architecture of Atlanto-Mediterranean biota. Despite the acknowledged key role played by these historical events in shaping population genetic structure of marine species, little is still known about the processes involved in shaping the spatial distribution of genetic variation within intertidal species. We intended in this study to reconstruct the phylogeography of a common and widely distributed coastal species across the East Atlantic and Mediterranean Sea (the warty crab Eriphia verrucosa), aiming to unravel potential microevolutionary processes likely involved in shaping its genetic polymorphism. For this purpose, a total of 155 specimens of E. verrucosa from 35 locations across the entire distribution range were analyzed by comparing a 453 basepairs region of the mitochondrial gene cytochrome oxidase subunit 1 (Cox1).ResultsOur results unveiled the prevalence of high genetic connectivity among East Atlantic and Mediterranean populations, with noticeable genetic distinctiveness of the peripheral population from the Azores. Spatio-temporal patterns of genetic diversification and demographic history allowed retrieving genetic imprints of late Pleistocene vicariant event across the Gibraltar Strait followed by subsequent postglacial expansion events for both the East Atlantic and Mediterranean regions. Integrative evidences from the outcomes of comparison of regional genetic diversification, as well as evolutionary and biogeographic histories reconstructions, support the existence of potential glacial refugia for E. verrucosa in the East Atlantic and western Mediterranean. Our results also revealed low levels of genetic variability along with recent demographic and spatial expansion events for eastern Mediterranean warty crabs, suggesting that the eastern areas within the distribution range of the species might have been recently colonized from putative glacial refugia.ConclusionsThese findings provide new insights into the phylogeography and evolutionary history of a common but poorly studied Atlanto-Mediterranean decapod species. Specifically, they contribute to the understanding of the impact of historical processes on shaping contemporary population genetic structure and diversity in intertidal marine species.

Historical demography of Coereba flaveola on Puerto Rico

AbstractWe use contemporary genetic diversity to characterize the within-island population structure and historical demography of Bananaquits (Aves: Thraupidae: Coerebinae: Coereba flaveola) on the West Indian island of Puerto Rico (Greater Antilles). We relate periods of population expansion, from Puerto Rico across the Lesser Antilles, to the genetic architecture of the source population, and describe differentiation of populations within Puerto Rico. Lastly, we report comparable analyses of populations of Bananaquits on Jamaica and of a related species, the Black-faced Grassquit (Coerebinae: Tiaris bicolor), on Puerto Rico. We found differentiation among contemporary populations of Bananaquits within Puerto Rico and signatures of renewed demographic expansion in eastern Puerto Rico beginning ~100 kyr ago and, in the western portion of the island, ~40 kyr ago. Populations of T. bicolor on Puerto Rico exhibit similar structure to Bananaquits, while Bananaquits on Jamaica exhibit no differentiation among locations. Both T. bicolor and Jamaican C. flaveola provide mixed evidence of demographic expansion.

Predicting contemporary range‐wide genomic variation using climatic, phylogeographic and morphological knowledge in an ancient, unglaciated landscape

AbstractAimUnderstanding the spatial distribution of genetic variation across a species’ range is a central tenet in evolutionary biology and the ability to predict such patterns is valuable to conservation management. Genetic diversity and differentiation may be explained by present‐day niche centrality, historical processes, or morphological variation across a species’ range, yet few studies evaluate these factors concurrently. Moreover, there is a particular lack of knowledge of the influence of these factors in ancient, unglaciated landscapes of the Southern Hemisphere. We investigate these concepts for their influence upon spatial patterns of genetic variation in a widespread plant species in a southern biodiversity hotspot.LocationSouth‐western Australia.TaxonCalothamnus quadrifidus.MethodsWe use genotyping‐by‐sequencing to assess genome‐wide diversity and differentiation across the range of Calothamnus quadrifidus, a morphologically variable species that occurs over a wide geographic range in an ancient, unglaciated landscape. We correlated the patterns of genetic diversity and differentiation with those predicted under four hypotheses regarding effects of geographic centrality, climatic centrality, historical phylogeography and morphological subspecies.ResultsWe found spatial variation in genetic diversity and strong population structuring, and while each hypothesis was consistent with some of these patterns, no hypothesis predicted the full extent of genetic diversity or structure in C. quadrifidus.Main conclusionsOur results are indicative of a complex evolutionary history, with multiple factors shaping contemporary genetic variation in C. quadrifidus over time, rather than any one major driving factor. This is enabled by the greater capacity to build complex evolutionary signals in ancient, more stable landscapes like the southwest of Western Australia that are not as predictable as those within the younger, post‐glacial landscapes of the Northern Hemisphere. Finally, our study demonstrates the importance of using an interdisciplinary approach to understanding the spatial patterns of genetic variation across species’ ranges and the influence of ecological, geographical and historical factors.

Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions.

BackgroundComparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM).MethodsA literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner.ResultsMitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM.ConclusionThis study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic.

Migrant pool model of dispersal explains strong connectivity of Avicennia officinalis within Sundarban mangrove areas: Effect of fragmentation and replantation

The ability of mangrove trees to reproduce and disperse in highly dynamic tidal environments is reflected in the contemporary genetic diversity and structure of their populations. Resilience and establishment may occur through either local recruitment (propagule pool model) or over longer distances with mixed origins (migrant pool model), thereby affecting the connectivity between natural populations. Anthropogenic activities such as encroachment and fragmentation or from mitigating reforestation could cause strategy switches and thus the connectivity and genetic structure of populations. In this study, we considered Avicennia officinalis, a dominant component of the Sundarban mangrove forest in Bangladesh to estimate dispersal dynamics over various distances within estuaries. A total of 423 individuals of A. officinalis, distributed over thirteen sites in the Sundarbans were sampled at both large and fine-scaled spatial level, the latter for comparison of natural and dense with fragmented sites. Up to 62 alleles showed a comparable level of allele diversity and gene diversities at both juvenile and adult life stages, assuming overall high levels of outcrossing. Significant inbreeding levels and high kinship values were solely observed at a reforested A. officinalis site. Genetic variables revealed high levels of connectivity between sites at close vicinity, with only a weak structure over larger geographic distances, between natural core Sundarban and coastal edge populations. Kinship coefficients were mostly low though significant up to several kilometers along estuarine branches, thereby suggesting propagule dispersal beyond each site. A fine-scaled analysis of kinship levels estimated for fragmented and natural forest plots along both sides of a river revealed that fragmentation induced higher kinship levels over 25–50 m distance, whereas dense natural populations were composed of less related individuals at shortest distances. A. officinalis populations might stay resilient through a mixture of unrelated propagules, clearly adhering a migrant pool model in natural sites and propagule pool model in fragmented sites. A poor gene diversity of planted trees might jeopardize the sustainability of mangrove plantation practices. Furthermore, high levels of diversity and connectivity indicated that the core Sundarban populations are a relevant source of germplasm in afforestation programmes.

Strong fluctuations in aboveground population size do not limit genetic diversity in populations of an endangered biennial species

Assessing genetic diversity within populations of rare species and understanding its determinants are crucial for effective species protection. While a lot is known about the relationships between genetic diversity, fitness, and current population size, very few studies explored the effects of past population size. Knowledge of past population size may, however, improve our ability to predict future population fates. We studied Gentianella praecox subsp. bohemica, a biennial species with extensive seed bank. We tested the effect of current, past minimal and maximal population size, and harmonic mean of population sizes within the last 15years on genetic diversity and fitness. Maximum population size over the last 15years was the best predictor of expected heterozygosity of the populations and was significantly related to current population size and management. Plant fitness was significantly related to current as well as maximum population size and expected heterozygosity. The results suggested that information on past population size may improve our understanding of contemporary genetic diversity across populations. They demonstrated that despite the strong fluctuations in population size, large reductions in population size do not result in immediate loss of genetic diversity and reduction of fitness within the populations. This is likely due to the seed bank of the species serving as reservoir of the genetic diversity of the populations. From a conservation point of view, this suggests that the restoration of small populations of short-lived species with permanent seed bank is possible as these populations may still be genetically diverse.

Role of colonization history and species‐specific traits on contemporary genetic variation of two salamander species in a Holocene island‐mainland system

AbstractAimInvestigate the role of colonization history and life history traits on contemporary patterns of genetic variation in two salamander species in a Holocene island‐mainland system.LocationRías Baixas, north‐western Spain.MethodsWe analysed mitochondrial and species‐specific nuclear markers (eight microsatellite markers) in 16 populations of Salamandra salamandra and Lissotriton boscai. Contemporary gene flow patterns between mainland and island populations were evaluated by migration analyses, whereas approximate Bayesian computation (ABC) was used to assess colonization history of insular populations of both species.ResultsLand bridge populations of both species exhibited reduced genetic diversity and increased genetic structure compared to mainland populations. ABC analysis showed that insular populations of both species were established by vicariance rather than by colonization via dispersal. We did not find evidence for contemporary gene flow, though the L. boscai insular population of Sálvora showed genetic admixture with mainland populations.Main conclusionsThis study supports the role of genetic drift in driving contemporary genetic variation of small and isolated populations. Other interplaying factors (e.g. island size, bathymetry) seemed to influence genetic variation, highlighting the importance of integrative studies to better understand the evolutionary dynamics of land bridge populations of amphibians.

Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers.

Amazonia is a major world centre of plant domestication, but little is known about how the crops were dispersed across the region. Manioc (Manihot esculenta) was domesticated in the south-western Amazon basin, and is the most important staple food crop that originated in Amazonia. Current contrasting distributions may reflect distinct histories of dispersal of bitter and sweet manioc landraces. To produce new insights into the evolutionary history of the crop, we investigated the contemporary genetic diversity and structure of bitter and sweet manioc along major Amazonian rivers. The patterns of genetic structure and diversity of wild and cultivated sweet and bitter manioc with four chloroplast and 14 nuclear microsatellite markers were evaluated. Results were interpreted in terms of the crop's dispersal. No phylogeographic patterns among rivers were detected, and genetic structure among rivers was confounded by the bitter-sweet divergence. However, differences in the distribution of nuclear diversity and somewhat distinctive patterns of genetic structure across rivers were observed within bitter and sweet manioc. Various pre-Columbian and post-European conquest events in the history of Amazonian occupation may explain the absence of clearer patterns of genetic structure. However, the wide distribution of the most common chloroplast haplotype agrees with an early dispersal of manioc across Brazilian Amazonia. Furthermore, differences in genetic structure and in the spatial distribution of genetic diversity suggest that bitter and sweet manioc had distinct dispersal histories. Knowledge about how prehistoric and contemporary Amazonian peoples manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native crops.

Recent transitions in genetic diversity and structure in the endangered semi‐natural grassland butterfly, Melitaea protomedia, in Japan

Abstract The monitoring of genetic characters and definition of effective conservation units are important for conservation of endangered semi‐natural grassland species. Using molecular markers, we elucidated the recent transitions in genetic diversity for the endangered grassland butterfly Melitaea protomedia (Lepidoptera; Nymphalidae) in Japan. First, we examined changes in genetic diversity and structure from the 1980s to the 2010s from archival and contemporary DNA samples using eight microsatellite markers. Second, we estimated the genetic structure based on 1374 bp of mitochondrial COI gene from contemporary samples. We also defined the conservation units of M. protomedia based on the above analysis. The genetic diversity of M. protomedia has significantly declined from the 1980s to the 2010s. Although genetic differentiation was very strong among populations in c. 2010, there was only weak genetic structure in c. 1990. In addition, the number of haplotypes based on mitochondrial DNA is now very low due to recent declines. These findings suggest that effective conservation units for critically endangered species should be determined based on historic (i.e. prior to population declines) as well as contemporary genetic diversity and differentiation, because genetic structure may have changed over time. Genetic analysis of archival DNA is useful to obtain historic genetic information.

Genetic diversity in envelope genes of contemporary U.S. porcine reproductive and respiratory syndrome virus strains influences viral antigenicity

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases in swine caused by porcine reproductive and respiratory syndrome virus (PRRSV). Genome sequences of sixty-six PRRSV strains were obtained using metagenomic sequencing of serum samples collected in the U.S. in 2014 to explore contemporary genetic diversity. Phylogenetic analysis of the genes encoding the envelope proteins identified four to eight distinct lineages with >87% intraclade identity. To explore the effect of the observed genetic diversity on antigenicity, the genome regions encoding either GP2a-GP3-GP4 or GP5-M in strain SD95-21 were replaced with alleles from each of eight distinct PRRSV strains using reverse genetics. The GP2a-GP3-GP4 region from only four of the eight strains yielded viable recombinant virus. When viable, both GP2a-GP3-GP4 and GP5-M variably affected antigenicity. A strain-dependent significant loss in cross reactivity was variably observed by indirect immunofluorescence assays using antisera from pigs vaccinated with commercial modified-live vaccines following replacement of GP2a-GP3-GP4 or GP5-M. Significantly reduced neutralization titers were similarly measured using antisera from naturally PRRSV-exposed pigs. These results illustrate the need to consider genomic regions besides GP5 for PRRSV epidemiology and vaccination.

Inferring Demographic History Using Two-Locus Statistics.

Population demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci. To leverage such patterns, we developed a composite-likelihood framework for inferring demographic history from aggregated statistics of pairs of loci. Using this framework, we show that two-locus statistics are more sensitive to demographic history than single-locus statistics such as the AFS. In particular, two-locus statistics escape the notorious confounding of depth and duration of a bottleneck, and they provide a means to estimate effective population size based on the recombination rather than mutation rate. We applied our approach to a Zambian population of Drosophila melanogaster Notably, using both single- and two-locus statistics, we inferred a substantially lower ancestral effective population size than previous works and did not infer a bottleneck history. Together, our results demonstrate the broad potential for two-locus statistics to enable powerful population genetic inference.

Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe.

Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.

Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America

BackgroundAvian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health.MethodsIn this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007–2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America.ResultsOur results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes.ConclusionsWe identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral dynamics for this infectious agent in wild bird populations.

A molecular portrait of maternal sepsis from Byzantine Troy.

Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.

Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes.

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M.capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks in the past. Previous studies identified conflicting mtDNA genetic substructuring patterns and thus contrasting evolutionary trajectories for both species. Using 10 microsatellite loci, the control region of mtDNA and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in the two species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N=2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581<HE <0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for M.paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, M.capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (FST =0.063, P<0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymetry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M.capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fishes.

MtDNA and Y‐chromosomal diversity in the Chachapoya, a population from the northeast Peruvian Andes‐Amazon divide

The ancient Chachapoya were an aggregate of several ethnic groups that shared a common language, religion, and material culture. They inhabited a territory at the juncture of the Andes and the Amazon basin. Their position between those ecozones most likely influenced their genetic composition. We attempted to better understand their population history by assessing the contemporary genetic diversity in the Chachapoya and three of their immediate neighbors (Huancas, Jivaro, and Cajamarca). We inferred signatures of demographic history and genetic affinities, and contrasted the findings with data from other populations on local and continental scales. We studied mitochondrial DNA (mtDNA; hypervariable segment [HVSI and HVSII]) and Y chromosome (23 short tandem repeats (STRs)) marker data in 382 modern individuals. We used Sanger sequencing for mtDNA and a commercially available kit for Y-chromosomal STR typing. The Chachapoya had affinities with various populations of Andean and Amazonian origin. When examining the Native American component, the Chachapoya displayed high levels of genetic diversity. Together with other parameters, for example, large Tajima's D and Fu's Fs, the data indicated no drastic reduction of the population size in the past. The high level of diversity in the Chachapoya, the lack of evidence of drift in the past, and genetic affinities with a broad range of populations in the Americas reflects an intricate population history in the region. The new genetic data from the Chachapoya indeed seems to point to a genetic complexity that is not yet resolved but beginning to be elucidated. Am. J. Hum. Biol. 28:857-867, 2016. © 2016Wiley Periodicals, Inc.