Intraspecific phylogeography in the sedge frog Litoria fallax (Hylidae) indicates pre-Pleistocene vicariance of an open forest species from eastern Australia

The eastern sedge frog Litoria fallax (Anura: Hylidae) is common throughout the open forests and coastal wetlands along the eastern coast of Australia. Its range spans four biogeographical zones from northern Queensland to central New South Wales. Phylogenetic analysis of mitochondrial DNA (mtDNA) haplotypes of 87 L. fallax individuals from 22 populations identified two major mtDNA lineages, differing by 11-12% sequence divergence. The two clades of haplotypes were separated by the McPherson Range, indicating that this mesic upland area has acted as a major long-term barrier to gene flow for this open forest species. Slight isolation by distance was observed within both the northern and southern lineages but was insufficient to explain the large sequence divergence between lineages. Within the northern lineage, additional phylogeographical structure was observed across the relatively dry Burdekin Gap which separates Atherton populations from all populations in the central and eastern Queensland biogeographical zones. There was less phylogeographical structure in the southern lineage suggesting historical gene flow across the drier portions of the Great Dividing Range. These data, together with recent observations of deep phylogeographical divergences in rainforest-restricted Litoria suggest that the east coast hylids of Australia represent an old (Tertiary) radiation. Individual species of Litoria have been strongly affected by climatic and ecological barriers to gene flow during the Quaternary.     

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.     

Spatial expansion and population structure of the neotropical malaria vector, Anopheles darlingi (Diptera: Culicidae)

Extensive population structuring is known to occur in Anopheles darlingi , the primary malaria vector of the Neotropics. We analysed the phylogeographic structure of the species using the mitochondrial cytochrome oxidase I marker. Diversity is divided into six main population groups in South America: Colombia, central Amazonia, southern Brazil, south-eastern Brazil, and two groups in north-east Brazil. The ancestral distribution of the taxon is hypothesized to be central Amazonia, and there is evidence of expansion from this region during the late Pleistocene. The expansion was not a homogeneous front, however, with at least four subgroups being formed due to geographic barriers. As the species spread, populations became isolated from each other by the Amazon River and the coastal mountain ranges of south-eastern Brazil and the Andes. Analyses incorporating distances around these barriers suggest that the entire South American range of An. darlingi is at mutation–dispersal–drift equilibrium. Because the species is distributed throughout such a broad area, the limited dispersal across some landscape types promotes differentiation between otherwise proximate populations. Moreover, samples from the An. darlingi holotype location in Rio de Janeiro State are substantially derived from all other populations, implying that there may be additional genetic differences of epidemiological relevance. The results obtained contribute to our understanding of gene flow in this species and allow the formulation of human mosquito health protocols in light of the potential population differences in vector capacity or tolerance to control strategies.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 854–866.     

Incongruence of morphology and genetic markers in Hyles tithymali (Lepidoptera: Sphingidae) from the Canary Islands

Hyles t. tithymali on the Canary Islands has been observed to occur in two larval morphotypes, connected by intermediate forms along a geographical cline from east to west. In this study, it was tested whether this distribution of phenotypes reflects a genealogical division of the population. mtDNA sequence data (COI + II, tRNA-leu) and genomic fingerprints from intersimple sequence repeat (ISSR)-PCR data were used. The sequence data had low variation (max. 0.4%), and phylogenetic analyses did not reveal groups that correlated with the morphotype. The samples did not group according to their island of origin and the most common haplotype was shared among all islands. Although nine haplotypes occurred only on the westernmost islands, the data showed little phylogeographical structure. The population of H. t. tithymali appears to reflect a comparatively rapid and recent colonization event of the Canary Islands. The ISSR-PCR data were very variable and did not reveal patterns corresponding to morphological variation or geographical distribution. Although the two morphs observed may represent the first stage of differentiation between two lineages, the recent origin of H. t. tithymali provided insufficient time for complete lineage sorting of ancestral polymorphism. Hence, the population of Hyles t. tithymali on the Canary Islands appears genetically more homogeneous than that was expected from the phenotypic distribution of the two morphotypes in the population.     

Population structuring in the monogonont rotifer Synchaeta pectinata: high genetic divergence on a small geographical scale

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Genetic diversity and population structure of the commercially harvested sea urchin Paracentrotus lividus (Echinodermata, Echinoidea)

The population structure of the edible Atlanto-Mediterranean sea urchin Paracentrotus lividus is described by analysing sequence variation in a fragment of the mitochondrial gene cytochrome c oxidase subunit I in 127 individuals from 12 localities across south-west Europe. The study revealed high levels of genetic diversity but low levels of genetic structure, suggesting a large degree of gene flow between populations and panmixis within each, the Mediterranean and Atlantic basins. However, we found significant genetic differentiation between the two basins probably due to restricted gene flow across the geographical boundary imposed by the area of the Strait of Gibraltar. Populations of P. lividus appeared to have experienced a recent demographic expansion in the late Pleistocene. We provide new evidence on the population structure of this commercial species, predicting a healthy stock of this sea urchin on the Mediterranean and Atlantic coasts.     

Consequences of the last glacial maximum on Nyctelia confusa (Coleoptera: Tenebrionidae) in Patagonia

The Last Glacial Maximum (LGM) has affected the population size and spatial distribution of a number of organisms in southern Patagonia. It has been hypothesized that species were able to persist in isolated refuges, which has generated processes of population expansion and genetic structure of populations after the LGM. In the present study, we evaluate these hypotheses and their association with local morphotypes in the endemic species Nyctelia confusa, a coleopteran that has low vagility and restricted distribution in the region. Accordingly, sixty‐nine specimens were sequenced for the gene for mitochondrial cytochrome c oxidase I. Effective population size was estimated through time, along with population structure and the phylogenetic signal of the morphs. The results suggest the existence of recent population expansion (10 Kyr BP), although there was no evidence of population structure or the phylogenetic signal for the described morphs. We propose that, during the LGM, N. confusa survived in multiple refuges, probably in the oriental slopes of the Andes range. The surviving populations would have expanded once the steppe was re‐established after the glaciers receded. This may have produced various secondary contact zones, homogenizing the genetic diversity, which would explain the observed pattern of panmixia. The morphological differentiation reported previously may be a result of local ecological adaptation not associated with the historical events of the LGM.     

Phylogeography of a pearl oyster (Pinctada maxima) across the Indo‐Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo‐West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene was analysed in 367 individuals sampled from nine populations across the Indo‐West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ_ST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 632–646.     

Brazilian populations of Drosophila maculifrons (Diptera: Drosophilidae): low diversity levels and signals of a population expansion after the Last Glacial Maximum

The Quaternary period was marked by considerable changes in climate. Such palaeoclimatic changes affected the population dynamics of many species, both in the Northern and in the Southern Hemisphere. However, the extent of these impacts on the demographic patterns of Neotropical species presenting different ecological requirements remains unclear. Drosophila maculifrons DUDA 1947 belongs to the guaramunu group of Drosophila and represents a potential indicator of the genetic consequences caused by the climatic fluctuations of the Quaternary, because it seems to be sensitive to temperature and humidity shifts. The aim of this study was to evaluate the evolutionary processes subjacent to the patterns of intraspecific diversity and structure of different populations of D. maculifrons. In total, 152 individuals were collected in the south and south‐east Brazil. Phylogenetic and phylogeographical analyses were performed based on sequences of COI and COII mitochondrial genes. In general, the results pointed to Brazilian populations of D. maculifrons being extremely impoverished in terms of mitochondrial diversity and population structure, which could be explained by a recent population expansion event dated to approximately 12 000 years ago. In fact, with the assistance of species palaeo‐distribution modelling strategies, it was possible to infer that most of the sampled region did not present the D. maculifrons environmental suitability requirements at least during the period of the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 55–66.     

Asymmetric dispersal of southern bull‐kelp (Durvillaea antarctica) adults in coastal New Zealand: testing an oceanographic hypothesis

Coastal populations are often connected by unidirectional current systems, but the biological effects of such asymmetric oceanographic connectivity remain relatively unstudied. We used mtDNA analysis to determine the phylogeographic origins of beach‐cast bull‐kelp (Durvillaea antarctica) adults in the Canterbury Bight, a 180 km coastal region devoid of rocky‐reef habitat in southern New Zealand. A multi‐year, quantitative analysis supports the oceanographically derived hypothesis of asymmetric dispersal mediated by the north‐flowing Southland Current. Specifically, 92% of beach‐cast specimens examined had originated south of the Bight, many drifting north for hundreds of kilometres, and some traversing at least 500 km of ocean from subantarctic sources. In contrast, only 8% of specimens had dispersed south against the prevailing current, and these counter‐current dispersers likely travelled relatively small distances (tens of kilometres). These data show that oceanographic connectivity models can provide robust estimates of passive biological dispersal, even for highly buoyant taxa. The results also indicate that there are no oceanographic barriers to kelp dispersal across the Canterbury Bight, indicating that other ecological factors explain the phylogeographic disjunction across this kelp‐free zone. The large number of long‐distance dispersal events detected suggests drifting macroalgae have potential to facilitate ongoing connectivity between otherwise isolated benthic populations.     

Phylogeography of the rock partridge (Alectoris graeca)

We used mitochondrial DNA control-region and microsatellite data to infer the evolutionary history and past demographic changes in 332 rock partridges (Alectoris graeca) sampled from throughout the species' distribution range, with the exception of the central Balkans region. Maternal and biparental DNA markers indicated concordantly that rock partridge populations are structured geographically (mtDNA phiST = 0.86, microsatellite FST = 0.35; RST = 0.31; P < 0.001). Phylogenetic analyses of 22 mtDNA haplotypes identified two major phylogroups (supported by bootstrap values = 93%), splitting partridges from Sicily vs. all the other sampled populations at an average Tamura-Nei genetic distance of 0.035, which corresponds to 65% of the average distance between closely related species of Alectoris. Coalescent estimates of divergence times suggested that rock partridges in Sicily were isolated for more than 200000 years. This deep subdivision was confirmed by multivariate, Bayesian clustering and population assignment analyses of microsatellite genotypes, which supported also a subdivision of partridges from the Alps vs. populations in the Apennines, Albania and Greece. Partridges in the Apennines and Albania-Greece were probably connected by gene flow since recently through a late Pleistocene Adriatic landbridge. Deglaciated Alps were probably colonized by distinct and, perhaps, not yet sampled source populations. Bottleneck and mismatch analyses indicate that rock partridges have lost variability through past population declines, and did not expand recently. Deglaciated areas could have been recolonized without any strong demographic expansion. Genetic data partially supported subspecies subdivisions, and allowed delimiting distinct conservation units. Rock partridges in Sicily, formally recognized as A. g. whitakeri, met the criteria for a distinct evolutionary significant unit.     

Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae,Rhodophyta) from New Zealand

Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct “cryptic” species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa.     

Genetic divergence, population structure and historical demography of rare springsnails (Pyrgulopsis) in the lower Colorado River basin

Springsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.     

Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia)

Phylogeographic patterns of intraspecific variation can provide insights into the population-level processes responsible for speciation and yield information useful for conservation purposes. To examine phylogeography and population structure in a migratory passerine bird at both continental and regional geographical scales, we analysed 344 bp of mitochondrial DNA (mtDNA) control region sequence from 155 yellow warblers (Dendroica petechia) collected from seven locations across Canada and from Alaska. There is a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) populations which appears to have developed during the recent Pleistocene. Some localities within these two regions also differ significantly in their genetic composition, suggesting further subdivision on a regional geographical scale. Eastern and western birds form distinct phylogeographic entities and the clustering of all western haplotypes with two eastern haplotypes suggests that the western haplotypes may be derived from an eastern lineage. Analyses based on coalescent models support this explanation for the origin of western haplotypes. These results are consistent with important features of Mengel's model of warbler diversification. From a conservation perspective they also suggest that individual populations of migrant birds may form demographically isolated management units on a smaller scale than previously appreciated.     

Molecular phylogeny of the genus Apatrobus (Coleoptera: Carabidae: Patrobinae) in western Japan

We performed a molecular phylogenetic analysis of the ground beetles Apatrobus (Carabidae), endemic to Japan, using the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 28S rRNA (28S) genes. We focused on the species divergence in Kyushu, Shikoku and western Honshu and used 15 of 19 species and three populations with undetermined species in the DNA analysis. The gene trees showed that, of the Apatrobus species studied, A. hayachinensis Nakane from northern Honshu was not included in the monophyletic group of the other Apatrobus species and likely to be of a different genus. Divergence time estimation suggested that Apatrobus species excluding A. hayachinensis diverged 5.2 million years ago and the subsequent divergence of species occurred during the Pliocene and Pleistocene. In each of the main islands, Kyushu, Shikoku and Honshu, two or more distinct lineages occurred and all species had restricted distribution areas, suggesting that ancient dispersal and vicariance among the three main islands resulted in the nested biogeographical pattern of species distribution.     

Phylogeography of the smooth snake Coronella austriaca (Serpentes: Colubridae): evidence for a reduced gene pool and a genetic discontinuity in Central Europe

The present study considers the genetic structure and phylogeography of the smooth snake (Coronella austriaca) in Central Europe, as analyzed on the basis of 14 microsatellite markers and a 284‐bp fragment of cytochrome b. We found deep divergence between western and south‐eastern Poland, suggesting at least two different colonization routes for Central Europe, originating in at least two different refugia. The west/south‐east divide was reflected in the haplotype distribution and topology of phylogenetic trees as defined by mitochondrial DNA, and in population structuring seen in the admixture analysis of microsatellite data. The well supported western European clade suggests that another refugium might have existed. We also note the isolation‐by‐distance and moderate‐to‐pronounced structuring in the examined geographical demes. Our data fit the assumption of the recently suggested sex‐biased dispersal, in that we found a strong divide in the maternal line, as well as evidence for a small but existent gene flow based on biparentally inherited microsatellite markers. All studied populations were very similar in respect of allelic richness, observed and expected heterozygosities, and inbreeding coefficients. However, some genetic characteristics were different from those expected compared to a similar fine‐scale study of C. austriaca from Great Britain. In the present study, we observed heterozygosity deficit, high inbreeding, and low Garza–Williamson indices, suggesting a reduction in population size. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 195–210.     

Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single‐nucleotide polymorphism data

Marine systems have traditionally been thought of as “open” with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star Ophionotus victoriae to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. Ophionotus victoriae possesses feeding planktotrophic larvae with presumed high dispersal capability, but a previous study revealed genetic structure along the Antarctic Peninsula. To test the extent of genetic differentiation within O. victoriae, we sampled from the Ross Sea through the eastern Weddell Sea. Whereas two mitochondrial DNA markers (16S rDNA and COI) were employed to allow comparison to earlier work, a 2b‐RAD single‐nucleotide polymorphism (SNP) approach allowed sampling of loci across the genome. Mitochondrial data from 414 individuals suggested three major lineages, but 2b‐RAD data generated 1,999 biallelic loci that identified four geographically distinct groups from 89 samples. Given the greater resolution by SNP data, O. victoriae can be divided into geographically distinct populations likely representing multiple species. Specific historical scenarios that explain current population structure were examined with approximate Bayesian computation (ABC) analyses. Although the Bransfield Strait region shows high diversity possibly due to mixing, our results suggest that within the recent past, dispersal processes due to strong currents such as the Antarctic Circumpolar Current have not overcome genetic subdivision presumably due to historical isolation, questioning the idea of large open circumpolar populations in the Southern Ocean.     

Phylogeography of the yucca moth Tegeticula maculata: the role of historical biogeography in reconciling high genetic structure with limited speciation

Tegeticula maculata is one of the most ancient and morphologically variable lineages within the yucca moths, yet has apparently undergone little diversification in comparison with much younger yucca moth lineages that have rapidly diversified. A phylogeographic approach was used to determine the number of independent lineages within T. maculata and to examine whether these patterns corresponded with morphological differences between its subspecies maculata and extranea. Phylogenetic analysis of mitochondrial DNA sequence variation indicated that the two subspecies are in separate clades, but there was also an equally deep split within subspecies maculata. There was no evidence for gene flow among regions and there was considerable substructure within clades. The phylogeographic structure of moth populations among and within subspecies can be explained in part by historical biogeographic boundaries and increasingly patchy postglacial distribution of the exclusive host plant, Hesperoyucca whipplei. Local specialization and co-adaptation would be possible in the absence of apparent gene flow, yet gross morphological divergence is limited to the very old split between the subspecies. Sorting of ancient mitochondrial lineages followed by local genetic differentiation may explain the pattern of high genetic structure with limited speciation.     

Foundations for conservation of intraspecific genetic diversity revealed by analysis of phylogeographical structure in the endangered endemic lizard Podarcis lilfordi

Aim  To describe and analyse phylogeographical patterns in the endangered endemic lizard Podarcis lilfordi from across its remaining range and thereby establish baseline information on genetic diversity that will help determine conservation priorities and assist future reintroduction programs.
Location  Balearic Islands, Spain.
Methods  We analysed mitochondrial DNA (2382 bp sequence from eight genes) from 118 individuals and characterized the relationships among haplotypes using parsimony networks, as well as phylogenetic inference. Analyses of historical gene flow and population growth were used to provide further insights into population histories.
Results  Four unconnected parsimony networks were obtained that mirrored the main clades in the phylogenetic tree: (I) all Menorcan populations, (II) Dragonera, Malgrats and Toro islands (Western Mallorca) (III and IV) and the remaining populations from Cabrera and Mallorca. Two major haplotype groups were detected in Menorca (I) and these provided signatures of a demographic expansion and asymmetrical historical gene flow, respectively, concordant with the expected direction of colonization from south to north of the island. Populations from western Mallorca (II) showed evidence of historical allopatric fragmentation events following isolation around the start of the Pleistocene. In networks III and IV, Cabreran populations appear to have become isolated from north and south Mallorca quite recently, with asymmetric gene flow indicating a northwards dispersal direction.
Main conclusions  P. lilfordi is a genetically diverse species that shows substantial mtDNA structuring both between regions and, at a finer scale, between some islet populations within regions. The precarious state of some islet populations shown here to be quite divergent (e.g. Toro island in western Mallorca) means that conservation of this intraspecific biodiversity requires urgent action.     

Spatial patterns of genetic structure among populations of a stone‐cased caddis (Trichoptera: Tasimiidae) in south‐east Queensland,Australia

1. Gene flow and dispersal among populations of a stone‐cased caddis (Tasimiidae: Tasimia palpata) were estimated indirectly using a 460 bp region of the cytochrome oxidase I gene of mitochondrial DNA. 2. There was no significant differentiation at the largest spatial scale (between catchments) and no correlation between genetic distance and geographic distance. These results are consistent with widespread adult dispersal. 3. Conversely, significant genetic differentiation was detected at the smallest spatial scale examined (among reaches within streams). This pattern was primarily because of significant F_ST values in a single stream (Bundaroo Creek). 4. Bundaroo Creek also had the lowest mean number of haplotypes per population (n = 7) suggesting that a limited number of females may be responsible for recruitment at these sites. Significant F_ST's at the reach scale may be a result of this ‘patchy’ recruitment. However, additional evidence regarding the long‐range dispersal ability and fecundity of T. palpata females is needed to test this hypothesis fully.