Population Divergence Times Research Articles

Estimation of Population Divergence Times from Non-Overlapping Genomic Sequences: Examples from Dogs and Wolves

Despite recent technological advances in DNA sequencing, incomplete coverage remains to be an issue in population genomics, in particular for studies that include ancient samples. Here, we describe an approach to estimate population divergence times for non-overlapping sequence data that is based on probabilities of different genealogical topologies under a structured coalescent model. We show that the approach can be adapted to accommodate common problems such as sequencing errors and postmortem nucleotide misincorporations, and we use simulations to investigate biases involved with estimating genealogical topologies from empirical data. The approach relies on three reference genomes and should be particularly useful for future analysis of genomic data that comprise of nonoverlapping sets of sequences, potentially from different points in time. We applied the method to shotgun sequence data from an ancient wolf together with extant dogs and wolves and found striking resemblance to previously described fine-scale population structure among dog breeds. When comparing modern dogs to four geographically distinct wolves, we find that the divergence time between dogs and an Indian wolf is smallest, followed by the divergence times to a Chinese wolf and a Spanish wolf, and a relatively long divergence time to an Alaskan wolf, suggesting that the origin of modern dogs is somewhere in Eurasia, potentially southern Asia. We find that less than two-thirds of all loci in the boxer and poodle genomes are more similar to each other than to a modern gray wolf and that--assuming complete isolation without gene flow--the divergence time between gray wolves and modern European dogs extends to 3,500 generations before the present, corresponding to approximately 10,000 years ago (95% confidence interval [CI]: 9,000-13,000). We explicitly study the effect of gene flow between dogs and wolves on our estimates and show that a low rate of gene flow is compatible with an even earlier domestication date ∼30,000 years ago (95% CI: 15,000-90,000). This observation is in agreement with recent archaeological findings and indicates that human behavior necessary for domestication of wild animals could have appeared much earlier than the development of agriculture.

Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co‐distributed species

Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent-based inferences about demographic processes to reconstruct the population histories of two co-distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N.lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P.miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N.lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P.miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation.

Genetic isolation of insular populations of the Maghrebian bat, Myotis punicus, in the Mediterranean Basin

AbstractAim We investigate the population genetic structure of the Maghrebian bat, Myotis punicus, between the mainland and islands to assess the island colonization pattern and current gene flow between nearby islands and within the mainland.Location North Africa and the Mediterranean islands of Corsica and Sardinia.Methods We sequenced part of the control region (HVII) of 79 bats across 11 colonies. The phylogeographical pattern was assessed by analysing molecular diversity indices, examining differentiation among populations and estimating divergence time. In addition, we genotyped 182 bats across 10 colonies at seven microsatellite loci. We used analysis of molecular variance and a Bayesian approach to infer nuclear population structure. Finally, we estimated sex‐specific dispersal between Corsica and Sardinia.Results Mitochondrial analyses indicated that colonies between Corsica, Sardinia and North Africa are highly differentiated. Within islands there was no difference between colonies, while at the continental level Moroccan and Tunisian populations were highly differentiated. Analyses with seven microsatellite loci showed a similar pattern. The sole difference was the lack of nuclear differentiation between populations in North Africa, suggesting a male‐biased dispersal over the continental area. The divergence time of Sardinian and Corsican populations was estimated to date back to the early and mid‐Pleistocene.Main conclusions Island colonization by the Maghrebian bats seems to have occurred in a stepping‐stone manner and certainly pre‐dated human colonization. Currently, open water seems to prevent exchange of bats between the two islands, despite their ability to fly and the narrowness of the strait of Bonifacio. Corsican and Sardinian populations are thus currently isolated from any continental gene pool and must therefore be considered as different evolutionarily significant units (ESU).

Diffusion Approximations for Demographic Inference: DaDi

AbstractModels of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia, building the most complex statistically well-characterized model of human migration out of Africa to date.

The phylogeographic architecture of the fucoid seaweed Ascophyllum nodosum: an intertidal ‘marine tree’ and survivor of more than one glacial–interglacial cycle

AbstractAim Ascophyllum nodosum (L.) Le Jolis is a dominant fucoid seaweed occurring along sheltered, rocky shores throughout the North Atlantic (but not in the Pacific), where it is a foundational species of the intertidal community. Its large size and vulnerability to ice‐scour have led to the hypothesis that contemporary populations in the north‐west Atlantic may be the result of de novo recolonization from the north‐east Atlantic since the Last Glacial Maximum (LGM) (c. 20 ka). We tested this hypothesis.Location Temperate North Atlantic rocky intertidal between c. 42 and 65° N latitude.Methods More than 1300 individuals from 28 populations were sampled from across the entire range of A. nodosum and genotyped for six microsatellite loci, and > 500 individuals were genotyped for two mitochondrial loci, an intergenic spacer (IGS) and the tRNA (W) gene (trnW). Population structure and historical demography were analysed in a standard population genetics and coalescence framework.Results Based on the presence of private alleles and haplotypes, we found that A. nodosum has survived on both sides of the Atlantic (since before the LGM, dating back to at least the penultimate Eemian interglacial) with similar effective population sizes and divergence times (1.2 and 0.8 Ma). Dispersal has been predominantly from Europe to North America, and there is very weak present‐day population differentiation across the North Atlantic. Diversity measures provided additional support for determining the location of refugia.Main conclusions Ascophyllum nodosum was apparently little affected by the LGM, although contemporary climate change is likely to have major effects on its latitudinal distribution on both sides of the North Atlantic. It is a very long‐lived species, analogous in virtually all demographic aspects to a tree – resistant to extinction but vulnerable to catastrophic events. The Brittany peninsula is a hotspot of genetic diversity worthy of conservation.

Erratum to: Patterns of mtDNA diversity in North Atlantic populations of the mussel Mytilus edulis

The post-colonization direction of gene flow in Fig. 5 was reversed. Although this mistake alters some conclusions regarding post-colonization gene flow (p. 405), IM-derived estimates of population splitting (s) and divergence times are correct as reported and these data form the basis for the major conclusions regarding routes of colonization. The recombinant haplotype from Mahone NS is 677 not 667.

How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study

Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.

Historical Divergence and Gene Flow in the Genus Zea

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence--and ultimately speciation--remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticated Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last approximately 150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.

A well-tested set of primers to amplify regions spread across the avian genome

1. IntroductionDNA markers have been used to examine a broad range ofbiological problems, including those in phylogen etics, populationgenetics and the identiÞcatio n of individuals. Nuclear loci providea rich source of information regarding evolutionary history andthey allow researche rs to examine many unlinked markers thathave the potential to provide insight the coalescent process as wellas introgress ion or hybridizatio n events (e.g. Maddison, 1997; Nic-hols, 2001 ). Information about the nuclear genome can be collectedby sequencing or by examining single nucleotide polymorphis ms(SNPs) (Sunnucks, 2000; Avise, 2004 ). Unlike mitochondr ialregions where virtually universal primers are available for verte-brates (e.g., Sorenson et al., 1999 ), extensively tested primer setsfor nuclear regions that are likely to work on the majority of spe-cies within a group are not available.In phylogenetic studies, nuclear sequence data have providedadditional insights into avian evolution (e.g., Avise, 2004; Hackettet al., 2008 ). The nuclear genome is heterogeneous , consisting ofcoding regions, introns, untranslated regions (UTRs), andintergeni c regions. The markers exhibit varying patterns of molec-ular evolution (e.g., mutation rates, base composition, etc.), andthus can be used at a variety of different taxonomi c levels for dif-ferent types of phylogeneti c questions. In addition to substitution alvariation , non-coding regions often exhibit length variation , pro-viding indel (insertionÐdel etion) characters that can be added tothe regionOs information content (e.g., Fain and Houde, 2004 ).Populatio n-level questions can be examined using non-codingregions such as introns. Substitutional (and indel) variation of mul-tiple individuals of a single species or a set of closely relatedspecies provide insights into population divergence times andancestral population sizes (e.g., Jennings and Edwards, 2005;Aitken et al., 2004 ). SNPs present in these rapidly evolving regionsare increasingly being used as markers because they provide anopportun ity to assess a large number of unlinked loci for a rangeof population questions (BrumÞeld et al., 2003; Morin et al.,2004 ). In addition to population genetics, SNPs also have thepotential to be used in parentage studies and for quantitativegenetic studies in wild populations.In birds, there are several studies which have published sets ofprimers to amplify nuclear regions, particularly intron regions (e.g.,Friesen et al., 1999, 1997; Primmer et al., 2002; Waltari andEdwards, 2002; Slade et al., 1993; Backstršm et al., 2008 ). How-ever, many of these primers have been tested on a limited set of

Lutzomyia longipalpis s.l. in Brazil and the impact of the Sao Francisco River in the speciation of this sand fly vector

Lutzomyia longipalpis s.l. (Diptera: Psychodidae) is the principal vector of Leishmania infantum chagasi in the Americas, and constitutes a complex of species. Various studies have suggested an incipient speciation process based on behavioral isolation driven by the chemotype of male sexual pheromones. It is well known that natural barriers, such as mountains and rivers can directly influence population divergence in several organisms, including insects. In this work we investigated the potential role played by the Sao Francisco River in eastern Brazil in defining the current distribution of Lu. longipalpis s.l. Our studies were based on analyses of polymorphisms of the cytochrome b gene (cyt b) sequences from Lu. longipalpis s.l. available in public databases, and from additional field-caught individuals. Altogether, 9 distinct populations and 89 haplotypes were represented in the analyses. Lu. longipalpis s.l. populations were grouped according to their distribution in regards to the 10°S parallel: north of 10°S (<10°S); and south of 10°S (>10°S). Our results suggest that although no polymorphisms were fixed, moderate genetic divergences were observed between the groups analyzed (i.e., FST = 0.184; and Nm = 2.22), and were mostly driven by genetic drift. The population divergence time estimated between the sand fly groups was about 0.45 million years (MY), coinciding with the time of the change in the course of the Sao Francisco River, during the Mindel glaciation. Overall, the polymorphisms on the cyt b haplotypes and the current speciation process detected in Lu. longipalpis s.l. with regards to the distribution of male sexual pheromones suggest a role of the Sao Francisco River as a significant geographical barrier in this process.

Pleistocene speciation of sister taxa in a North Pacific clade of brooding sea stars (Leptasterias)

Although numerous coastal marine species show intra-specific lineage splitting and population divergence times that date to the period of glacial cycles during the Pleistocene epoch, reported instances of recent speciation in the coastal marine environment are relatively rare. Marine organisms with brood-protection and other reproductive modes with limited dispersal potential have been suggested to experience more frequent speciation and extinction events than related species with higher dispersal rates, but few studies have actually estimated divergence times of sister species in these organisms. Here, two mitochondrial gene regions (cytochrome oxidase subunit I, putative control region and upstream tRNAs) and a nuclear gene region (Elongation factor 1α subunit intron 4) provide evidence of recent (0.5–1.2 Mya) cladogenetic events in four pairs of putative sister taxa in a predominantly North Pacific brooding subgenus of sea stars (Leptasterias subgenus Hexasterias). Calibration is obtained from a trans-arctic migration in a related clade of sea stars (Leptasterias subgenera Hexasterias and Nesasterias) that is timed to the opening of the Bering Strait at 3.5 ± 0.25 Mya, and uncertainty in the calibration point is accommodated with a normally-distributed Bayesian prior probability. Similar estimates of population splitting times for two of the pairs of putative sister taxa were obtained by a multilocus coalescent analysis. Estimates of mitochondrial mutation rates (0.01/My) were approximately 50% of the values calibrated for sister species pairs in tropical sea stars and sea urchins.

Recent Range Expansion and Divergence among North American Prairie Grouse

Prairie grouse (genus: Tympanuchus) once existed throughout much of North America but have recently experienced significant population declines, isolation, and extinction. In previous molecular studies, contrasting patterns or an unresolved polytomy among Tympanuchus taxa (Tympanuchus phasianellus, Tympanuchus pallidicinctus, and Tympanuchus cupido) have resulted from traditional phylogenetic methods. As an alternative approach, the timing of expansion and the demographic processes that may have lead to this association among haplotypes, namely incomplete lineage sorting or migration, were explicitly investigated by comparing pairwise mitochondrial DNA control region nucleotide differences and through the use of a isolation with migration coalescent model. The timing of geographic expansion and population divergence time estimates generated under these models support previous inferences that Tympanuchus experienced a rapid expansion and diversification in the late Pleistocene 10,000-80,000 years before present. Further, morphological and behavioral differences originally used to describe Tympanuchus species were substantiated with little or no migration identified since population divergence. However, estimates of population divergence and migration between a number of morphologically similar subspecific taxa, including the greater prairie chicken (Tympanuchus Cupido pinnatus), the endangered Attwater's prairie chicken (Tympanuchus Cupido attwateri), and the extinct heath hen (Tympanuchus Cupido cupido), suggest these taxa are as differentiated with each other as they are from other Tympanuchus species. This information will prove useful in conservation efforts by providing estimates of demographic history that have helped shape the evolutionary relationships among Tympanuchus grouse.

Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow From Mitochondrial, X and Y Chromosome Resequencing Data

We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25-50 individuals from each of 10 human populations. Application of a coalescent-based Markov chain Monte Carlo technique allows simultaneous inference of divergence times, rates of gene flow, as well as changes in effective population size. Results from comparisons between sub-Saharan African and Eurasian populations estimate that 1500 individuals founded the ancestral Eurasian population approximately 40 thousand years ago (KYA). Furthermore, these small Eurasian founding populations appear to have grown much more dramatically than either African or Oceanian populations. Analyses of sub-Saharan African populations provide little evidence for a history of population bottlenecks and suggest that they began diverging from one another upward of 50 KYA. We surmise that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations. African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian populations.

Co‐phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities

Comparative microevolutionary studies of multiple parasites occurring on a single host species can help shed light on the processes underlying parasite diversification. We compared the phylogeographical histories, population genetic structures and population divergence times of three co-distributed and phylogenetically independent ectoparasitic insect species, including an amblyceran and an ischnoceran louse (Insecta: Phthiraptera), a hippoboscid fly (Insecta: Diptera) and their endemic avian host in the Galápagos Islands. The Galápagos hawk (Aves: Falconiformes: Buteo galapagoensis) is a recently arrived endemic lineage in the Galápagos Islands and its island populations are diverging evolutionarily. Each parasite species differed in relative dispersal ability and distribution within the host populations, which allowed us to make predictions about their degree of population genetic structure and whether they tracked host gene flow and colonization history among islands. To control for DNA region in comparisons across these phylogenetically distant taxa, we sequenced ~1 kb of homologous mitochondrial DNA from samples collected from all island populations of the host. Remarkably, the host was invariant across mitochondrial regions that were comparatively variable in each of the parasite species, to degrees consistent with differences in their natural histories. Differences in these natural history traits were predictably correlated with the evolutionary trajectories of each parasite species, including rates of interisland gene flow and tracking of hosts by parasites. Congruence between the population structures of the ischnoceran louse and the host suggests that the ischnoceran may yield insight into the cryptic evolutionary history of its endangered host, potentially aiding in its conservation management.

Phylogeographic analysis of the chloroplast DNA variation in wild common bean (Phaseolus vulgaris L.) in the Americas

The wild common bean (Phaseolus vulgaris) is widely but discontinuously distributed from northern Mexico to northern Argentina on both sides of the Isthmus of Panama. Little is known on how the species has reached its current disjunct distribution. In this research, chloroplast DNA polymorphisms in seven non-coding regions were used to study the history of migration of wild P. vulgaris between Mesoamerica and South America. A penalized likelihood analysis was applied to previously published Leguminosae ITS data to estimate divergence times between P. vulgaris and its sister taxa from Mesoamerica, and divergence times of populations within P. vulgaris. Fourteen chloroplast haplotypes were identified by PCR-RFLP and their geographical associations were studied by means of a Nested Clade Analysis and Mantel Tests. The results suggest that the haplotypes are not randomly distributed but occupy discrete parts of the geographic range of the species. The current distribution of haplotypes may be explained by isolation by distance and by at least two migration events between Mesoamerica and South America: one from Mesoamerica to South America and another one from northern South America to Mesoamerica. Age estimates place the divergence of P. vulgaris from its sister taxa from Mesoamerica at or before 1.3 Ma, and divergence of populations from Ecuador-northern Peru at or before 0.6 Ma. As these ages are taken as minimum divergence times, the influence of past events, such as the closure of the Isthmus of Panama and the final uplift of the Andes, on the migration history and population structure of this species cannot be disregarded.

Effects of recent population bottlenecks on reconstructing the demographic history of prairie‐chickens

Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and MDIV). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (theta), population divergence time (t), and time to the most recent common ancestor (TMRCA) from MDIV were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history.

Genetic signature of recent glaciation on populations of a near‐shore marine fish species (Syngnathus leptorhynchus)

Continental glaciation has played a major role in shaping the present-day phylogeography of freshwater and terrestrial species in the Northern Hemisphere. Recent work suggests that coastal glaciation during ice ages may have also had a significant impact on marine species. The bay pipefish, Syngnathus leptorhynchus, is a near-shore Pacific coast fish species with an exceptionally wide latitudinal distribution, ranging from Bahia Santa Maria, Baja California to Prince William Sound, Alaska. Survey data indicate that S. leptorhynchus is experiencing a range expansion at the northern limit of its range, consistent with colonization from southern populations. The present study uses six novel microsatellite markers and mitochondrial DNA (mtDNA) sequence data to study the present-day population genetic structure of four coastal populations of S. leptorhynchus. Deficits in mtDNA and nuclear DNA diversity in northern populations from regions glaciated during the last glacial maximum (LGM) [c. 18 000 years before present (bp)] suggest that these populations were effected by glacial events. Direct estimates of population divergence times derived from both isolation and isolation-with-migration models of evolution are also consistent with a postglacial phylogenetic history of populations north of the LGM. Sequence data further indicate that a population at the southern end of the species range has been separated from the three northern populations since long before the last interglacial event (c. 130 000 years bp), suggesting that topographical features along the Pacific coast may maintain population separation in regions unimpacted by coastal glaciation.

SPECIATIONAL HISTORY OF AUSTRALIAN GRASS FINCHES (POEPHILA) INFERRED FROM THIRTY GENE TREES

Multilocus genealogical approaches are still uncommon in phylogeography and historical demography, fields which have been dominated by microsatellite markers and mitochondrial DNA, particularly for vertebrates. Using 30 newly developed anonymous nuclear loci, we estimated population divergence times and ancestral population sizes of three closely related species of Australian grass finches (Poephila) distributed across two barriers in northern Australia. We verified that substitution rates were generally constant both among lineages and among loci, and that intralocus recombination was uncommon in our dataset, thereby satisfying two assumptions of our multilocus analysis. The reconstructed gene trees exhibited all three possible tree topologies and displayed considerable variation in coalescent times, yet this information provided the raw data for maximum likelihood and Bayesian estimation of population divergence times and ancestral population sizes. Estimates of these parameters were in close agreement with each other regardless of statistical approach and our Bayesian estimates were robust to prior assumptions. Our results suggest that black-throated finches (Poephila cincta) diverged from long-tailed finches (P. acuticauda and P. hecki) across the Carpentarian Barrier in northeastern Australia around 0.6 million years ago (mya), and that P. acuticauda diverged from P. hecki across the Kimberley Plateau-Arnhem Land Barrier in northwestern Australia approximately 0.3 mya. Bayesian 95% credibility intervals around these estimates strongly support Pleistocene timing for both speciation events, despite the fact that many gene divergences across the Carpentarian region clearly predated the Pleistocene. Estimates of ancestral effective population sizes for the basal ancestor and long-tailed finch ancestor were large (about 521,000 and about 384,000, respectively). Although the errors around the population size parameter estimates are considerable, they are the first for birds taking into account multiple sources of variance.

Population Divergence Times and Historical Demography in red Knots and Dunlins

AbstractWe employed Bayesian coalescent modeling of samples of mitochondrial control region sequences in two species of shorebird, Red Knots (Calidris canutus) and Dunlins (Calidris alpina) to estimate evolutionary effective population size, population divergence times, and time to most recent common ancestor of genes in the samples. The gene trees for the two species contrast sharply: knot haplotypes were connected in a shallow, star phylogeny whereas Dunlin haplotypes were related in a deeper bifurcating genealogy. Divergence times of populations representing all six subspecies of knots are estimated to have occurred within the last 20 000 (95% CI: 5600–58 000) years, and evolutionary effective population sizes of females are small (Nef = 2000–14 000). We hypothesized that breeding knots were restricted to unglaciated regions of Eurasia during the last glacial maximum, and gradually expanded eastwards into Alaska, the high Canadian Arctic and Greenland as the ice melted. Population divergence times in Dunlins are much older (58 000–194 000 ybp) and effective population size has historically been higher in major lineages (Nef = 12 000–44 000). We conclude that Dunlin populations were not severely reduced in size in the last 200 000 years, and major lineages have differentiated under restricted gene flow for a much longer time than knots. Knots present a snapshot of genetic evolution in the last 20 000 years, whereas Dunlins display patterns of genetic evolution over an order of magnitude longer time frame.Tiempos de Divergencia Poblacional e Historia Demográfica en Calidris canutus y C. alpinaResumen. Aplicamos modelos Bayesianos de coalescencia en una muestra de secuencias de la región de control mitocondrial de dos especies de playeros, Calidris canutus y C. alpina, para estimar el tamaño efectivo de la población, los tiempos de divergencia entre poblaciones y la distancia cronológica al antepasado común más reciente de los genes muestreados. Los árboles genealógicos de las dos especies contrastan fuertemente: los haplotipos de C. canutus están conectados superficialmente siguiendo un patrón filogenético en forma de estrella, mientras que los haplotipos de C. alpina se relacionan de manera más profunda, mostrando patrones de genealogía bifurcados. Se estima que la divergencia poblacional de las seis subespecies de C. canutus tuvo lugar durante los últimos 20 000 años aproximadamente, y los tamaños efectivos de la población de hembras son pequeños (Nef = 2000–14 000). Presumimos que la reproducción de C. canutus estuvo restringida sólo a regiones de Eurasia que estuvieron libres de hielo durante el último máximo glacial y se expandieron gradualmente hacia el este de Alaska, el Ártico canadiense y Groenlandia cuando el hielo se derritió. Los tiempos de divergencia poblacional en C. alpina son más antiguos (58 000–194 000), y el tamaño efectivo de la población ha sido históricamente más alto en los linajes principales (Nef = 12 000–44 000). Concluimos que las poblaciones de C. alpina no mostraron reducciones serias en los últimos 200 000 años, y que sus linajes se han diferenciado por un período de tiempo mucho más prolongado que los de C. canutus. Los patrones encontrados para C. canutus representan una imagen de evolución genética ocurrida durante los últimos 20 000 años, mientras que los patrones de C. alpina indican la ocurrencia de evolución genética durante un período de tiempo diez veces más largo.

The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.