The influence of interaction type and feeding location on the phylogeographic structure of the yucca moth community associated with Hesperoyucca whipplei

The interactions between herbivorous insects and their host plants have been central in generating diversification in both groups. We used a community of four yucca moth species, monophagous on the host plant Hesperoyucca whipplei (Agavaceae), to examine how the type of interaction and where insects feed within a plant influence phylogeographic structure of herbivorous insects. These four species included two fruit-feeders, one mutualistic and one commensalistic, and two commensalistic stalk-feeders. Surveys based on mtDNA cytochrome oxidase I sequence data demonstrated that the moth species differed in phylogeographic history. Populations of the mutualist pollinator, Tegeticula maculata, exhibited the most subdivision in comparison to the three commensal Prodoxus species (both genera in Lepidoptera, Prodoxidae). Feeding location was also correlated with differences in phylogeographic history through its influence on population sizes and the probability of gene flow. The results suggest that both the outcome of interactions and where insects feed may influence population structure.     

Genetic differentiation and phylogeography of gulls in the Larus cachinnans–fuscus group (Aves: Charadriiformes)

We studied mitochondrial genetic differentiation among nine taxa of large gulls of the Larus cachinnans-fuscus group, which form part of the circumpolar Herring Gull complex. Our primary interest was to see if there were unrecognized gene flow barriers, to what extent mitochondrial genetic population structure conformed to current taxonomic boundaries, and what it might reveal about possible differences in population history. Sequences (430 nucleotides) of the hypervariable control region I (HVR-I) were obtained from 580 individuals and proved highly informative within this recently diverged group of birds. Contrary to current classification, a basal split was revealed between an Atlantic-Mediterranean clade (atlantis, michahellis, armenicus) and a NW Palearctic-Central Asian clade (cachinnans, barabensis, mongolicus, fuscus-group). There was almost no mitochondrial gene flow between these two groups, although they are in geographical contact in two areas (eastern North Atlantic, Black Sea). Within each of the two major groups, there was strong phylogeographic structure with gene flow barriers between some neighbouring taxa (e.g. cachinanns vs. barabensis), but also a case of poor genetic differentiation between phenotypically distinct forms (barabensis vs. heuglini). At the subspecies level, current taxonomy corresponded well to molecular genetic structure: over 80% of the molecular genetic variance was partitioned among six (groups of) taxa. This is in sharp contrast to previous studies using allozymes and amplified fragment length polymorphism (AFLP) markers, which seemed to indicate extensive nuclear gene flow. Within-taxon haplotype phylogenies and mismatch distributions revealed contrasting demographic histories: cachinnans (Ponto-Caspian region) and atlantis (NE Atlantic) represent ancient lineages with large long-term population sizes, inland forms stem from very recent colonization events (barabensis, mongolicus) or passed through a population bottleneck (armenicus).     

Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.     

Phylogeographic structure in the bogus yucca moth Prodoxus quinquepunctellus (Prodoxidae): comparisons with coexisting pollinator yucca moths

The pollination mutualism between yucca moths and yuccas highlights the potential importance of host plant specificity in insect diversification. Historically, one pollinator moth species, Tegeticula yuccasella, was believed to pollinate most yuccas. Recent phylogenetic studies have revealed that it is a complex of at least 13 distinct species, eight of which are specific to one yucca species. Moths in the closely related genus Prodoxus also specialize on yuccas, but they do not pollinate and their larvae feed on different plant parts. Previous research demonstrated that the geographically widespread Prodoxus quinquepunctellus can rapidly specialize to its host plants and may harbor hidden species diversity. We examined the phylogeographic structure of P. quinquepunctellus across its range to compare patterns of diversification with six coexisting pollinator yucca moth species. Morphometric and mtDNA cytochrome oxidase I sequence data indicated that P. quinquepunctellus as currently described contains two species. There was a deep division between moth populations in the eastern and the western United States, with limited sympatry in central Texas; these clades are considered separate species and are redescribed as P. decipiens and P. quinquepunctellus (sensu stricto), respectively. Sequence data also showed a lesser division within P. quinquepunctellus s.s. between the western populations on the Colorado Plateau and those elsewhere. The divergence among the three emerging lineages corresponded with major biogeographic provinces, whereas AMOVA indicated that host plant specialization has been relatively unimportant in diversification. In comparison, the six pollinator species comprise three lineages, one eastern and two western. A pollinator species endemic to the Colorado Plateau has evolved in both of the western lineages. The east-west division and the separate evolution of two Colorado Plateau pollinator species suggest that similar biogeographic factors have influenced diversification in both Tegeticula and Prodoxus. For the pollinators, however, each lineage has produced a monophagous species, a pattern not seen in P. quinquepunctellus.     

Phylogeography of a morphologically diverse Neotropical montane species, the Common Bush-Tanager (Chlorospingus ophthalmicus)

The Common Bush-Tanager (Chlorospingus ophthalmicus) is distributed in Neotropical cloud-forests from Mexico to Argentina and contains 25 subspecies divided into eight subspecies groups based on biogeography, eye coloration, presence of a postocular spot and chest band. All of Central America is occupied by a single subspecies group; whereas the Andes are believed to be occupied by seven additional subspecies groups. We used five mitochondrial genes to investigate the phylogeography and possible species limits of the ophthalmicus complex. A total of 14 monophyletic lineages were uncovered within the ophthalmicus complex, including three clades currently classified as separate species (C. semifuscus, inornatus and tacarcunae). Divergence estimates for these clades date between 0.8 and 5.2 million years ago (Ma). Contrary to expectations based on morphological diversity, phylogeographic structure was greatest in Mexico and Central America and weakest in the Andes. Morphological and genetic divergences were not significantly correlated and most morphologically defined subspecies groups were not supported. Our evidence suggests the ophthalmicus complex originated in Mexico ca. 6.0 Ma (million years ago) and spread south into the Andes ca. 4.7 Ma before the completion of the Isthmus of Panama. Three genetically divergent lineages of ophthalmicus that formed in the Andes possess a complex checkerboard distribution, with a single lineage represented by disjunct populations from Venezuela and the southern Andes, while intervening populations in Ecuador and Central Peru form two genetically and morphologically divergent lineages.     

Deep phylogeographic divisions and long‐term persistence of forest invertebrates (Hexapoda: Collembola) in the North‐Western Mediterranean basin

The North‐Western Mediterranean basin is well known for its high number of relictual endemic taxa, and has been indicated as one of the world’s major biodiversity hotspots at the species level. A possible contributing factor may be long‐term persistence of populations and their prolonged stability. This study was designed to investigate the phylogeographic structure of three common species of the genus Lepidocyrtus (Hexapoda: Collembola), soil‐dwelling arthropods characterized by limited dispersal capabilities and generally associated with forest habitats. We observed a remarkable geographic structure, with numerous deeply divergent genetic lineages occupying islands as well as mainland sites with no apparent gene flow among most sites, even across distances of only tens of kilometres. The reconstructed time frame for the evolution of these lineages suggests divergence between 5 and 15 Ma. This indicates a remarkably ancient origin and long‐term persistence of individual lineages over a fine geographic scale despite the occurrence of abrupt sea level and climatic fluctuations in the area. This further suggests that currently recognized morphological species might be a serious underestimation of the true springtail biodiversity within this region.     

A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea

New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.     

Testing species boundaries in an ancient species complex with deep phylogeographic history: genus Xantusia (Squamata: Xantusiidae)

Identification of species in natural populations has recently received increased attention with a number of investigators proposing rigorous methods for species delimitation. Morphologically conservative species (or species complexes) with deep phylogenetic histories (and limited gene flow) are likely to pose particular problems when attempting to delimit species, yet this is crucial to comparative studies of the geography of speciation. We apply two methods of species delimitation to an ancient group of lizards (genus Xantusia) that occur throughout southwestern North America. Mitochondrial cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 4 gene sequences were generated from samples taken throughout the geographic range of Xantusia. Maximum likelihood, Bayesian, and nested cladogram analyses were used to estimate relationships among haplotypes and to infer evolutionary processes. We found multiple well-supported independent lineages within Xantusia, for which there is considerable discordance with the currently recognized taxonomy. High levels of sequence divergence (21.3%) suggest that the pattern in Xantusia may predate the vicariant events usually hypothesized for the fauna of the Baja California peninsula, and the existence of deeply divergent clades (18.8%-26.9%) elsewhere in the complex indicates the occurrence of ancient sundering events whose genetic signatures were not erased by the late Wisconsin vegetation changes. We present a revised taxonomic arrangement for this genus consistent with the distinct mtDNA lineages and discuss the phylogeographic history of this genus as a model system for studies of speciation in North American deserts.     

Genomic variation patterns of subspecies defined by phenotypic criteria: Analyses of the mangrove species complex,Avicennia marina

Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation are expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina (Forssk.) Vierh. of the Indo-West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, whereas the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species-like patterns in some respects and population-like patterns in others. We propose that the subspecies designated in A. marina are informative in predicting genetic divergences and useful in making conservation decisions.     

Glacial vicariance and historical biogeography of rock ptarmigan (Lagopus mutus) in the Bering region

In this paper, we address alternative hypotheses for the evolution of subspecies of rock ptarmigan (Lagopus mutus) endemic to the Aleutian Archipelago. To do this we examined patterns of genetic differentiation among populations of rock ptarmigan in the Aleutian Islands and parts of both Alaska and Siberia. Variation in mitochondrial control region sequences of 105 rock ptarmigan from 10 subspecies within the Bering region revealed three major phylogenetic lineages, two of which are endemic to the Aleutian Islands. Accordingly, haplotype and nucleotide diversities of rock ptarmigan within the archipelago are much higher than within mainland Alaska or Siberia. For Aleutian rock ptarmigan, analyses of molecular variance indicated significant genetic structuring and low estimates of gene flow among populations, despite small interisland distances within the archipelago. However, isolation by distance did not describe the pattern of gene flow or differentiation at this scale. Our estimates of divergence times of lineages suggest that Aleutian rock ptarmigan became isolated prior to the most recent Pleistocene glaciation event (late Wisconsin Stade) and that current patterns of genetic variation reflect the postglacial redistribution of divergent lineages and subsequent limited gene flow. In addition, genetic divergence among lineages was concordant with the distribution of plumage types among subspecies. The patterns of genetic variation described here for rock ptarmigan provide evidence for the role of glacial vicariance in contributing to genetic diversity within this and other Bering region species.     

Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae)

We examined the consequences of barriers, stream architecture and putative dispersal capability on levels of genetic differentiation among populations of the freshwater fish Craterocephalus stercusmuscarum. Seven polymorphic allozyme loci and sequences of a 498-bp fragment of the ATPase 6 mitochondrial DNA (mtDNA) gene were used to assess patterns of genetic variation among 16 populations from upland and lowland streams of five drainages in northern Queensland, Australia. Concordant patterns at both genetic markers revealed that there were significant levels of genetic subdivision among all populations, while an analysis of molecular variation showed that the distribution of genetic diversity was not consistent with contemporary drainage structure. There were reciprocally monophyletic mtDNA clades and fixed or large frequency differences at allozyme loci either side of instream barriers such as waterfalls. This implied barriers were effective in restricting gene flow between upland and lowland populations separated by waterfalls. However, there were two genetically distinct groups in upland areas, even within the same subcatchment, as well as high levels of genetic subdivision among lowland populations, suggesting barriers alone do not explain the patterns of genetic diversity. The data revealed a complex phylogeographic pattern, which we interpreted to be the result of one or more invasion events of independent lineages to different sections of each drainage, possibly mediated by well documented geomorphological changes. Our results highlight the importance of earth structure and history in shaping population genetic structure in stream organisms where dispersal capability may be limited, and reveal that the contemporary structure of drainages is not necessarily a good indicator of genetic relationships among populations.     

Limiting cheaters in mutualism: evidence from hybridization between mutualist and cheater yucca moths

Mutualisms are balanced antagonistic interactions where both species gain a net benefit. Because mutualisms generate resources, they can be exploited by individuals that reap the benefits of the interaction without paying any cost. The presence of such 'cheaters' may have important consequences, yet we are only beginning to understand how cheaters evolve from mutualists and how their evolution may be curtailed within mutualistic lineages. The yucca-yucca moth pollination mutualism is an excellent model in this context as there have been two origins of cheating from within the yucca moth lineage. We used nuclear and mitochondrial DNA markers to examine genetic structure in a moth population where a cheater species is parapatric with a resident pollinator. The results revealed extensive hybridization between pollinators and cheaters. Hybrids were genetically intermediate to parental populations, even though all individuals in this population had a pollinator phenotype. The results suggest that mutualisms can be stable in the face of introgression of cheater genes and that the ability of cheaters to invade a given mutualism may be more limited than previously appreciated.     

Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies

The southeastern United States is a major phylogeographic break hotspot for amphibians, but the processes underlying this hotspot remain to be explicitly tested. We test the correlation of genetic lineages with subspecies breaks in the southeastern United States and the association of such breaks with climate, using Rana sphenocephala as a case study, and place our results in the broader context of the Alabama‐Appalachian suture zone (AL‐Appalachian SZ). We use genetic and ecological methods to (i) determine whether genetic lineages are coincident with the AL‐Appalachian SZ or the subspecies and (ii) test the correlation of major climatic breaks with genetic structure and morphological variation in R. sphenocephala. Bayesian phylogenetic analyses of the ND1 mtDNA gene and microsatellite cluster analyses revealed two distinct lineages with over 4% sequence divergence. The geographic distributions of the two lineages are concordant with the AL‐Appalachian SZ but do not correspond to the ranges of the subspecies based on morphology. Mantel tests revealed that isolation by distance and historical barriers to gene flow, rather than climate, are the major drivers of genetic divergence at neutral loci. Examination of climate breaks across the Southeast revealed a pattern incongruent with suture zone hotspots, suggesting that phylogenetic structure has been driven primarily by historical factors, such as isolation, the Appalachian Mountains and the Apalachicola/Chattahoochee/Flint River Basin. However, climate breaks are consistent with the geographic distribution of the subspecies of R. sphenocephala, suggesting that environmental pressures may be driving divergence in morphological traits that outpaces molecular evolution.     

新疆草兔的种群遗传结构和亚种分化

新疆草兔 (Lepus capensis) 的群体遗传结构至今无系统的研究报道,亚种水平的分类也长期存在争议.该文测定了形态分类上的新疆草兔3个亚种共87个个体的线粒体DNA (mtDNA)控制区(control region,D-Loop)592 bp的序列,经分析发现148个多态性位点,共定义了44个单倍型.新疆草兔的单倍型多样度(h,0.977 ± 0.005)和核苷酸多样度(π,0.064 ± 0.031)都较高,显示了较高的遗传多样性.分子变异分析(AMOVA)结果显示,4个地理群体间的显著分化可能是由地理隔离造成的.群体遗传结构分析显示,新疆草兔包含4个进化枝,并且每个进化枝都对应特定的分布区域,显示了明显的系统地理结构.该研究的结果支持形态分类上草兔西域亚种(L.c.lehmanni)的分类地位; 但中亚亚种(L.c.centrasiaticus)被分为两个独立的进化枝,提示可能存在两个亚种; 帕米尔亚种(L.c.pamirensis)与其他亚种间的遗传距离在13%以上,提示其可能已达到种的分化水平.     

Mitochondrial phylogeographic structure of the white-browed piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina

Aim Our understanding of the geographic patterns of gene flow between populations of birds in the Indo‐Malayan faunal region is surprisingly poor compared with that in other parts of the world. A thorough knowledge of general patterns of phylogeographic structure is, however, of utmost importance for conservation purposes. Species with poor dispersal capabilities could serve as indicators of endemism and genetic isolation in the Indochinese subregion. From their morphology (tiny size, short tail, short and rounded wings), piculets of the genus Sasia are inferred to have poor dispersal capabilities, and thus form a suitable focal species. This study analysed the pattern of genetic variation within the White‐browed Piculet (Sasia ochracea). Location Southeast Asia, north of the Isthmus of Kra. Methods We sampled 43 individuals throughout the breeding range of S. ochracea. DNA was extracted both from fresh tissues (n = 15) and from toe pads from ancient museum skins (n = 28). We amplified a 801‐bp fragment of the mitochondrial ND2 gene to reconstruct the phylogeographic history of the White‐browed Piculet. The sequence data were analysed using Bayesian inference, statistical parsimony, and population genetics methods (analysis of molecular variance, mismatch distributions). We estimated the amount of ongoing gene flow between populations using the coalescent‐based method implemented in Mdiv . Results The analysis of molecular variance indicated that the current taxonomy does not adequately reflect the amount of genetic variation within S. ochracea, as the great majority of genetic variation was nested within the nominal subspecies, which is distributed from Nepal to southern Vietnam. Bayesian inference analyses and haplotype networks suggested the occurrence of five main lineages that are strongly correlated with geography. Our coalescent‐based analyses indicated a very limited amount of ongoing gene flow between these five lineages. Our dating analyses suggested that the genetic structuring probably occurred during the last 400,000 years. Main conclusions Our analyses revealed that S. ochracea is composed of at least five lineages: south Vietnam (South Annam and ‘Cochinchina’), India and Nepal, Myanmar and India, the remainder of Indochina, and probably southern Myanmar (Tenasserim). We strongly recommend that studies aiming to understand the phylogeographic structure within Indo‐Malayan species sample these areas.     

Mitochondrial DNA phylogeography of Caiman crocodilus in Mesoamerica and South America

The Neotropical crocodylian species, Caiman crocodilus, is widely distributed through Mesoamerica, northern South America, and the Amazon basin. Four subspecies are recognized within C. crocodilus, suggesting some geographic variation in morphology. In this study, we utilized mitochondrial DNA (mtDNA) sequence data from 45 individuals of C. crocodilus throughout its range to infer its evolutionary history and population structure, as well as to evaluate genealogical support for subspecies and their geographic distributions. Our molecular phylogenetic results identified five mtDNA haplotype clades with a mean sequence divergence of 3.4%, indicating considerable evolutionary independence among phylogeographic lineages. Our results were also broadly consistent with current subspecific taxonomy, with some important additional findings. First, we found substantial genetic structuring within C. c. fuscus from southern Mesoamerica. Second, though we confirmed the existence of a widespread Amazonian clade, we also discovered a cryptic and divergent mtDNA lineage that was indistinguishable from C. c. crocodilus based on external morphology. Third, we confirm the status of C. c. chiapasius as a distinct evolutionary lineage, and provide evidence that C. c. fuscus may be moving northward and hybridizing with C. c. chiapasius in northern Mesoamerica. Finally, our results parallel previous phylogeographic studies of other organisms that have demonstrated significant genetic structure over shorter geographic distances in Mesoamerica compared with Amazonia. We support conservation efforts for all five independent lineages within C. crocodilus, and highlight the subspecies C. c. chiapasius as a unit of particular conservation concern.     

Phylogeography of white-spotted Charr (Salvelinus leucomaenis) inferred from mitochondrial DNA sequences

The white-spotted charr (Salvelinus leucomaenis) is a coldwater-adapted fish distributed in far-eastern Asia. To assess phylogeographic patterns of this species over most of its range in the Japanese archipelago and Sakhalin Island, Russia, we examined nucleotide sequences of the mitochondrial DNA (mtDNA) cytochrome b region (557 bp) in 141 individuals from 50 populations. A total of 33 (5.5%) nucleotide positions were polymorphic and defined 29 haplotypes. Phylogenetic analysis assigned the observed haplotypes to four main clades, which were characterized by the idiosyncrasies and discontinuity of geographic distributions. The nested clade analyses revealed that the geographical distribution patterns of some haplotypes and clades were explained by historical event such as past fragmentation. Although substantial genetic differentiation was found among the four main clades, their geographic distributions overlapped extensively in several regions. Since white-spotted charr can potentially use both freshwater and marine environments, coexistence among different lineages can be attributed to secondary contact through range expansion by migratory individuals during multiple glacial periods after interglacial isolation. Finally, our data demonstrate that the current subspecies designation does not reflect the phylogeography of this species based on mtDNA analysis. Hierarchical analysis (AMOVA) also showed that genetic variation was far more pronounced within subspecies than among subspecies (i.e., among discrete regions). These results suggest that each population, rather than each subspecies, must be treated as an evolutionarily significant unit.     

Random interbreeding between cryptic lineages of the Common Raven: evidence for speciation in reverse

DNA sequence studies frequently reveal evidence of cryptic lineages in morphologically uniform species, many of which turn out to be evolutionarily distinct species. The Common Raven (Corvus corax) includes two deeply divergent mtDNA lineages: one lineage seems restricted to western North America and the other is Holarctic in distribution. These deep clades hint of the possibility of cryptic species in the western United States. We tested this hypothesis in a population consisting of an equal proportion of both mtDNA clades, by quantifying mating patterns and associated fitness consequences with respect to mtDNA. We also tested for morphological, behavioural and ecological correlates of sex and mtDNA clade membership. Mate pairings were random with respect to mtDNA clades, and there were no differences in reproductive success between assortatively and nonassortatively mated pairs. We found no differences in survival or resource use between clades. There were no differences in morphological or behavioural characters between mtDNA clades, except one clade trended towards greater mobility. These results suggest there are no barriers to gene flow between mtDNA clades and argue that the mtDNA clades have remerged in this population, likely due to a lack of ecological or signal differentiation between individuals in each lineage. Hence, in Common Ravens, phylogeographic structure in mtDNA is a reflection of likely past isolation rather than currently differentiated species.     

Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: evidence for cryptic allopatric diversity

Underground environments are increasingly recognized as reservoirs of faunal diversity. Extreme environmental conditions and limited dispersal ability of underground organisms have been acknowledged as important factors promoting divergence between species and conspecific populations. However, in many instances, there is no correlation between genetic divergence and morphological differentiation. Lucifuga Poey is a stygobiotic fish genus that lives in Cuban and Bahamian caves. In Cuba, it offers a unique opportunity to study the influence of habitat fragmentation on the genetic divergence of stygobiotic species and populations. The genus includes four species and one morphological variant that have contrasting geographical distributions. In this study, we first performed a molecular phylogenetic analysis of the Lucifuga Cuban species using mitochondrial and nuclear markers. The mitochondrial phylogeny revealed three deeply divergent clades that were supported by nuclear and morphological characters. Within two of these main clades, we identified five lineages that are candidate cryptic species and a taxonomical synonymy between Lucifuga subterranea and Lucifuga teresinarum. Secondly, phylogeographic analysis using a fragment of the cytochrome b gene was performed for Lucifuga dentata, the most widely distributed species. We found strong geographical organization of the haplotype clades at different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. At a larger temporal scale, these processes could also explain the diversification and the distribution of the different species.     

Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analyses

Aim To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location Europe (mostly Italy). Methods We collected adult males from dung pats from 15 Italian localities over the period 2000–2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, F_ST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species.