Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.     

Biogeography of ‘Cyprinella lutrensis’: intensive genetic sampling from the Pecos River ‘melting pot’ reveals a dynamic history and phylogenetic complexity

Thorough sampling is necessary to delineate lineage diversity for polytypic ‘species’ such as Cyprinella lutrensis. We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study focussed on the Pecos River due to its complex geological history and potential to harbour multiple lineages. We used geometric–morphometric, morphometric, and meristic analyses to test for phenotypic divergence and combined nucDNA with mtDNA to test for cytonuclear disequilibrium and combined our sequences with published data to conduct a phylogenetic re‐assessment of the entire C. lutrensis clade. We detected five co‐occurring mtDNA lineages in the Pecos River, but no evidence for cytonuclear disequilibrium or phenotypic divergence. Recognized species were interspersed amongst divergent lineages of ‘C. lutrensis’. Allopatric divergence among drainages isolated in the Late Miocene and Pliocene apparently produced several recognized species and major divisions within ‘C. lutrensis’. Pleistocene re‐expansion and subsequent re‐fragmentation of a centralized lineage founded younger, divergent lineages throughout the Rio Grande basin and Edwards Plateau. There is also evidence of recent introductions to the Rio Grande, Pecos and South Canadian Rivers. Nonetheless, deeply divergent lineages have coexisted since the Pleistocene.     

A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity

The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys are urgently needed to avoid underestimating tropical diversity, and the use of mtDNA markers can be instrumental in identifying and prioritizing taxa for species discovery.     

Body Size Diversity and Frequency Distributions of Neotropical Cichlid Fishes (Cichliformes: Cichlidae: Cichlinae)

Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size diversity in Neotropical freshwater fishes. We test for divergence, phylogenetic autocorrelation and among-clade partitioning of body size space. Neotropical cichlids show low phylogenetic autocorrelation and divergence within and among taxonomic levels. Three distinct regions of body size space were identified from body size frequency distributions at various taxonomic levels corresponding to subclades of the most diverse tribe, Geophagini. These regions suggest that lineages may be evolving towards particular size optima that may be tied to specific ecological roles. The diversification of Geophagini appears to constrain the evolution of body size among other Neotropical cichlid lineages; non-Geophagini clades show lower species-richness in body size regions shared with Geophagini. Neotropical cichlid genera show less divergence and extreme body size than expected within and among tribes. Body size divergence among species may instead be present or linked to ecology at the community assembly scale.     

DEEP DIVERSIFICATION AND LONG‐TERM PERSISTENCE IN THE SOUTH AMERICAN ‘DRY DIAGONAL’: INTEGRATING CONTINENT‐WIDE PHYLOGEOGRAPHY AND DISTRIBUTION MODELING OF GECKOS

The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range‐wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American ‘dry diagonal’ biomes. Our approach couples traditional and model‐based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the ‘dry diagonal’ biomes. We recover extremely high genetic diversity and suggest that eight well‐supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low‐vagility species complexes, characterized by strong genetic structure and pre‐Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.     

Too strict or too loose? Integrative taxonomic assessment of Bombus lapidarius complex (Hymenoptera: Apidae)

The latest progress of the taxonomy is the use of integrative approach for species delimitation based on a multisource dataset. However, the taxonomic decision that should be made when convergence between the different lines of evidence is not observed remains debated. Here, we investigate the consequences of the application of an ‘integration by cumulation’ approach on the taxonomic statuses within the Bombus lapidarius complex when using an integrative taxonomic framework (i.e. nuclear and mitochondrial markers along with reproductive traits) compared with a strict ‘integration by congruence’ method. Our results show similar taxonomic conclusions whatever the decision-making approach used except for one taxon. According to the differentiation observed in our integrative taxonomic framework, recent divergence time and other field observations for this taxon, we assume that a too strict decision-making method could fail to detect recently diverged species. This is exemplified by the new species Bombus bisiculus sp. n. occurring in South Italy and Sicily.     

Species delimitation in the Chinese bamboo partridge Bambusicola thoracica (Phasianidae; Aves)

Although tropical and subtropical Asia harbour a high level of species diversity, their species richness can be underestimated because species which are in fact distinct have not been separately identified. In this study, we delimit Bambusicola thoracica into two full species, the Chinese bamboo partridge (B. thoracica) in continental Asia and the Taiwanese bamboo partridge (B. sonorivox) on the island of Taiwan, using coalescent‐based multilocus division and diagnosable vocalization patterns. Isolation‐with‐migration analysis indicated that the two bamboo partridges diverged approximately 1.8 million years ago, with gene flow present most probably during the early stages of their divergence. This conclusion supports the hypothesis that diverging lowland lineages spread across the Asian mainland, and continental islands have more opportunities for secondary contact than highland ones when the sea level was low. Our results imply that conservation of biodiversity in tropical and subtropical Asia could be hindered by overlooking numerous ‘hidden’ species and highlight the importance of re‐examining the taxonomic statuses of species in this region traditionally defined as polytypic.     

Pleistocene climatic cycling and diversification of the Andean treefrog, Hypsiboas andinus

Our understanding of the causes of diversification of Neotropical organisms lags behind that of Northern Hemisphere biota, especially for montane and temperate regions of southern South America. We investigated the mitochondrial DNA genealogical patterns in 262 individuals of the frog Hypsiboas andinus from 26 sites across the eastern ranges of the Andes Mountains in Argentina and Bolivia. Our phylogenetic analyses indicate at least three distinct lineages: one representing H. andinus from Northwestern Argentina and southern Bolivia, at least one H. andinus lineage from northern Bolivia, and one clade containing both H. andinus (from the southern portion of the species range) and its putative sister taxon Hypsiboas riojanus. Hypsiboas andinus samples from northern Bolivia are well differentiated and may represent distinct species. The northern Argentine H. andinus lineage and southern H. andinus/H. riojanus lineage likely diverged between 2 and 6 million years ago; their current sympatry may be the result of secondary contact due to range expansion after isolation during Andean uplift or may reflect cryptic species. Within the geographically extensive northern H. andinus clade, we found significant geographical structuring consistent with historical fragmentation and subsequent range expansion. The timing of this fragmentation and range expansion coincide with the Pleistocene, a time of extensive climatic cycling and vegetational shifts. Average divergence among clades is lower than those found for other Neotropical taxa, highlighting the potential importance of recent climatic history in diversification in the southern Andes.     

PHYLOGEOGRAPHIC STRUCTURE AND OUTBREEDING DEPRESSION REVEAL EARLY STAGES OF REPRODUCTIVE ISOLATION IN THE NEOTROPICAL ORCHID EPIDENDRUM DENTICULATUM

Phylogeographic studies provide an important framework for investigating the mechanisms operating during the earliest stages of speciation, as reproductive barriers can be examined among divergent lineages in a geographic context. We investigated the evolution of early stages of intrinsic postmating isolation among different populations and lineages of Epidendrum denticulatum, a Neotropical orchid distributed across different biomes in South America. We estimated genetic diversity and structure for both nuclear and plastid markers, using a haplotype network, differentiation tests, Bayesian assignment analysis, and divergence time estimates of the main lineages. Reproductive barriers among divergent lineages were examined by analyzing seed viability following reciprocal crossing experiments. Strong plastid phylogeographic structure was found, indicating that E. denticulatum was restricted to multiple refuges during South American forest expansion events. In contrast, significant phylogeographic structure was not found for nuclear markers, suggesting higher gene flow by pollen than by seeds. Large asymmetries in seed set were observed among different plastid genetic groups, suggesting the presence of polymorphic genic incompatibilities associated with cytonuclear interactions. Our results confirm the importance of phylogeographic studies associated with reproductive isolation experiments and suggest an important role for outbreeding depression during the early stages of lineage diversification.     

Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, <Emphasis Type="Italic">Eleutherodactylus ockendeni</Emphasis>

Background  

The forests of the upper Amazon basin harbour some of the world's highest anuran species richness, but to date we have only the sparsest understanding of the distribution of genetic diversity within and among species in this region. To quantify region-wide genealogical patterns and to test for the presence of deep intraspecific divergences that have been documented in some other neotropical anurans, we developed a molecular phylogeny of the wide-spread terrestrial leaflitter frog Eleutherodactylus ockendeni (Leptodactylidae) from 13 localities throughout its range in Ecuador using data from two mitochondrial genes (16S and cyt b; 1246 base pairs). We examined the relation between divergence of mtDNA and the nuclear genome, as sampled by five species-specific microsatellite loci, to evaluate indirectly whether lineages are reproductively isolated where they co-occur. Our extensive phylogeographic survey thus assesses the spatial distribution of E. ockendeni genetic diversity across eastern Ecuador.     

Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae: Mirbelieae) exhibit different evolutionary history

Genetic structure among disjunct population groups of Pultenaea pauciflora was assessed to determine the evolutionary history of this species as a basis for conservation management strategies. Analysis of individuals from all extant populations using 1737 amplified length polymorphism markers revealed two highly divergent genetic entities with strong geographical structuring. Populations located at Narrogin and Brookton clustered together in Bayesian assignment analysis with every individual optimally placed in a single cluster with complete membership. Genetic differentiation between populations in these two areas was very low. Populations at Boddington were highly divergent from those located at Narrogin and Brookton. All individuals from Boddington populations were optimally placed into a second cluster with complete membership. Populations located at Boddington maintain lower levels of allelic diversity, yet greater levels of mean heterozygosity than populations located at Narrogin and Brookton. The degree of genetic differentiation and different patterns of genetic diversity strongly suggest historical divergence and separate evolutionary influences on the two lineages that occur in different ecological habitat. These Evolutionary Significant Units are likely to represent two cryptic sister taxa in the extant populations currently recognized as P. pauciflora, and the reassessment of taxonomic and conservation status of both lineages is required. © 2013 State of Western Australia. Biological Journal of the Linnean Society © 2013 The Linnean Society of London     

Miocene divergence,phenotypically cryptic lineages,and contrasting distribution patterns in common lichen‐forming fungi (Ascomycota: Parmeliaceae)

Despite the recent advancements in recognizing diversity in lichen‐forming fungi, assessing the timing of diversification remains largely unexplored in these important fungal symbionts. To better understand the evolutionary processes driving diversification in common lichen‐forming fungi, we investigated the phylogeny and biogeography of the broadly distributed Melanelixia fuliginosa/M. glabratula group, using molecular data from six nuclear markers. Phylogenetic analyses of individual gene alignments and combined data provide strong evidence for five species‐level lineages within this species complex. Three of these lineages correspond to the previously described species M. fuliginosa, M. glabratula, and M. subaurifera. The remaining two lineages, ‘M. sp. 1’ and ‘M. sp. 2’, merit species recognition based on genealogical concordance. Both M. glabratula and M. subaurifera had broad intercontinental distributions, sharing identical haplotypes among intercontinental populations. Based on the current sampling, M. fuliginosa s.s. was represented exclusively by European material and was not collected in North America. ‘M. sp. 1’ was represented by collections from Scotland and Spain; and ‘M. sp. 2’ was represented by collections in California, USA. Environmental factors driving the contrasting distribution patterns in this group remain unknown. Divergence times estimated using a coalescence‐based multilocus species‐tree approach suggest that diversification within the M. fuliginosa/M. glabratula group occurred exclusively during the Miocene. The results of the present study indicate that phenotypically cryptic lichen‐forming fungal species‐level lineages may be relatively ancient and do not necessarily reflect recent divergence events. Furthermore, diagnosable phenotypic differences may be absent even millions of years after the initial divergence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Evidence of neotropical anuran community disruption on rice crops: a multidimensional evaluation

Agricultural expansion is a major driver of biodiversity loss, especially in the megadiverse tropics. Rice is among the world’s most important food crops, invariably affecting biodiversity worldwide. Although the effects of habitat conversion to rice crops on biodiversity are not completely understood, landscape modification often creates conditions that benefit some species and excludes others. We conducted an integrative evaluation of the effects that habitat conversion to irrigated rice crops has on anuran communities from a Cerrado-Amazon ecotone. We adopted a multidimensional approach to compare anuran communities from agricultural and pristine environments considering (i) taxonomic metrics; (ii) functional and phylogenetic diversity; (iii) selected and excluded traits and (iv) body condition indices. When compared to their pristine counterparts, agricultural waterbodies showed increased functional divergence and decreased species diversity and functional richness. Furthermore, agricultural anuran communities exhibited lower phylogenetic diversity. Nonetheless, taxonomic diversity did not vary significantly, suggesting that it should not be used without complementary metrics. Species with small range, habitat specialization, small clutches and large body size were excluded from rice crops. Furthermore, frogs showed lower body condition in crops than in pristine areas. Understanding how species traits correlate with specific responses to agriculture will allow better predictions of the functional effects of anthropogenic land-use. Maintaining high diversity in anthropogenic environments is important for ecosystem resilience because diverse communities are more likely to hold multiple species capable of contributing to ecological functions. Our results show that converting natural vegetation to irrigated rice crops drives many species to local extinction, and resilient species to exhibit lower body condition.     

Secondary contact followed by gene flow between divergent mitochondrial lineages of a widespread Neotropical songbird (Zonotrichia capensis)

Understanding how genetic and phenotypic differences that arise in geographically isolated populations influence the outcome of secondary contact advances our knowledge of speciation. In the present study, we investigate the secondary contact between divergent lineages of a widespread Neotropical songbird, the Rufous‐collared sparrow (Zonotrichia capensis). Zonotrichia capensis is morphologically and behaviourally diverse, and shows a pattern of lineage diversification produced by a Pleistocene expansion and colonization of South America from a probable Central American origin. Consistent with previous results, we find three lineages throughout the species range, showing between 1.5% and 2.5% divergence in mitochondrial control region sequences. These lineages come into secondary contact in the Dominican Republic, La Paz (Bolivia), and North‐eastern Argentina. We use DNA microsatellite data to study a broad secondary contact zone in North‐eastern Argentina, finding that Bayesian clustering analyses do not assign individuals to their respective mitochondrial lineages. Overall, we did not observe nuclear genetic discontinuities in the study area. We conclude that, if genetic, morphological, and/or cultural differences accumulated among lineages during isolation, they were insufficient to prevent gene flow after secondary contact. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 863–868.     

Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae)

Studies on Neotropical phylogeography have largely focused on lowland organisms. Because lowland and highland biotas have different histories and are likely affected by different processes influencing population differentiation, understanding Neotropical diversification requires detailed studies on montane taxa. We present the most comprehensive analysis of population differentiation conducted so far on a widespread group of Neotropical montane organisms, focusing on the evolutionary relationships and phylogeography of Buarremon brush-finches (Aves: Emberizidae) in montane areas from Mexico through Argentina. Sequences of mitochondrial and nuclear genes demonstrate that Buarremon is not monophyletic with respect to Arremon and Lysurus. Genetic structure revealed by mtDNA is strong in both B. brunneinucha and B. torquatus. Gene genealogies and nucleotide diversity indicate that B. brunneinucha originated in Mexico and later expanded to South America, where it followed one colonization route through the east, and one through the west of the continent. Differentiation among populations of B. torquatus was substantial, reaching 8% uncorrected sequence divergence within South America. Relationships among major lineages of B. torquatus were not fully resolved owing to rapid differentiation, but the occurrence of closely related taxa in distant locations suggests a complex history of diversification. Some Colombian populations of B. brunneinucha have affinities with populations from Venezuela and the East Andean slope of Ecuador and Peru, and others with those from the Pacific slope of Ecuador. Moreover, five divergent lineages of B. torquatus occur within Colombia, highlighting the importance of dense sampling in northwest South America for studies on diversification of widespread Neotropical lineages.     

Diversity and endemism of Murinae rodents in Thai limestone karsts

This study aims to investigate the species diversity of rodents living in karst ecosystems of Thailand. A survey has been conducted throughout Thailand, 122 karsts sampled and 477 Murinae rodents live-trapped. Phylogenetic reconstructions were carried out using two mitochondrial markers (cytb, COI). A sequence-based species delimitation method completed by the analysis of the level of genetic divergence was then applied to define species boundaries within our dataset. The phylogenetic position of Niviventer hinpoon was also investigated and sequences obtained from the holotype specimen of this species were used to reliably identify samples of N. hinpoon. A total of 12 described Murinae species, corresponding to 17 deeply divergent genetic lineages, were encountered in limestone karsts of Thailand. Our study revealed an important genetic diversity within the traditionally recognized species Maxomys surifer (four highly divergent genetic lineages), Leopoldamys neilli (two highly divergent genetic lineages) and Berylmys bowersi (two highly divergent genetic lineages). These species could be considered as species complex and require further taxonomic work. This study also provides valuable information on the distribution of the two rodent species endemic to limestone karsts of Thailand, L. neilli and N. hinpoon. Leopoldamys neilli was the most abundant species encountered in Thai karsts during our survey. However, L. neilli specimens from western Thailand are genetically highly divergent from the remaining populations of L. neilli and could represent a separate species. Niviventer hinpoon, phylogenetically closely related to N. fulvescens, is much rarer and its distribution limited to central Thailand. Most of the other captured species are typically associated with forest ecosystems. This study suggests that limestone karsts play a key role in the preservation of the rodent species endemic to such habitat, but they would also provide refuges for the forest-dwelling Murinae rodents in deforested regions.     

Allopatry as a Gordian Knot for Taxonomists: Patterns of DNA Barcode Divergence in Arctic-Alpine Lepidoptera

Many cold adapted species occur in both montane settings and in the subarctic. Their disjunct distributions create taxonomic complexity because there is no standardized method to establish whether their allopatric populations represent single or different species. This study employs DNA barcoding to gain new perspectives on the levels and patterns of sequence divergence among populations of 122 arctic-alpine species of Lepidoptera from the Alps, Fennoscandia and North America. It reveals intraspecific variability in the barcode region ranging from 0.00–10.08%. Eleven supposedly different species pairs or groups show close genetic similarity, suggesting possible synonymy in many cases. However, a total of 33 species show evidence of cryptic diversity as evidenced by the presence of lineages with over 2% maximum barcode divergence in Europe, in North America or between the two continents. Our study also reveals cases where taxonomic names have been used inconsistently between regions and exposes misidentifications. Overall, DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective.     

Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia Hylia prasina and Yellow-whiskered Greenbul Eurillas latirostris), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in Eurillas (～4.1 MY). In Western Bluebill Spermophaga haematina, relatively divergent eastern and western lineages (～1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin Stiphrornis erythrothorax, birds sampled within Ghana were from two highly divergent lineages (～1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (～0.36 MY). For both Hylia and Stiphrornis, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.     

Three deeply divided lineages of the freshwater mussel genus <Emphasis Type="Italic">Anodonta</Emphasis> in western North America

The surprising diversity and recent dramatic decline of freshwater mussels in North America have been well documented, although inventory efforts to date have been concentrated in the eastern United States. Unlike their eastern counterparts, western freshwater mussels have received comparatively little attention. The accurate identity of western lineages is a necessary component for future inventory, monitoring, and ecological work involving these taxa. Here we initiate a study involving the most speciose genus (Anodonta) in western North America, incorporating information about type localities and type specimen morphology and describing the discovery of three highly divergent lineages among four western Anodonta species. In a limited phylogenetic analysis, we find (1) that A. californiensis/nuttalliana and A.oregonensis/kennerlyi are distinct, highly divergent clades, and (2) that A. beringiana is more closely allied with A. woodiana, an Asian species, than either of the other two western North American clades. We were largely unable to resolve the placement of these three clades with respect to other anodontines, and suggest the need for a broader phylogenetic framework. We recommend, however, that the existence of these three deeply divergent groups be considered in the development of regional monitoring, conservation and research plans despite the taxonomic uncertainty.     

Testing hypotheses for genealogical discordance in a rainforest lizard

Genealogical discordance, or when different genes tell distinct stories although they evolved under a shared history, often emerges from either coalescent stochasticity or introgression. In this study, we present a strong case of mito‐nuclear genealogical discordance in the Australian rainforest lizard species complex of Saproscincus basiliscus and S. lewisi. One of the lineages that comprises this complex, the Southern S. basiliscus lineage, is deeply divergent at the mitochondrial genome but shows markedly less divergence at the nuclear genome. By placing our results in a comparative context and reconstructing the lineages' demography via multilocus and coalescent‐based approximate Bayesian computation methods, we test hypotheses for how coalescent variance and introgression contribute to this pattern. These analyses suggest that the observed genealogical discordance likely results from introgression. Further, to generate such strong discordance, introgression probably acted in concert with other factors promoting asymmetric gene flow between the mitochondrial and nuclear genomes, such as selection or sex‐biased dispersal. This study offers a framework for testing sources of genealogical discordance and suggests that historical introgression can be an important force shaping the genetic diversity of species and their populations.