Multispecies Coalescent Analyses Research Articles

The first known fossil Uma: ecological evolution and the origins of North American fringe-toed lizards

BackgroundFossil evidence suggests that extant North American lizard genera (north of Mexico) evolved during the Miocene. Although fossils of the clade Phrynosomatidae (spiny lizards and sand lizards) have been reported, there have been no previously described fossils of the fringe-toed sand lizards (Uma). In the extant biota, Uma inhabit arid deserts, and members of the western clade of Uma are restricted to sand dunes or other habitats containing fine-grained sand.ResultsI describe the first known fossil of Uma and refer the fossil to the total clade of Uma with an apomorphy-based diagnosis. The fossil is a partial premaxilla that was found in the Miocene strata of the Dove Spring Formation of southern California, dating to 8.77 Ma. The paleoenvironment of the Dove Spring Formation was semiarid and contained ephemeral streams that facilitated deposition, and there is no evidence of sand dune deposits in the strata containing the locality from which the Uma fossil was found. Divergence time analyses of a concatenated molecular dataset with four fossil calibrations support a Neogene origin of the total clade of Uma and of the crown clade of Uma. Those analyses also estimated a Neogene divergence between Uma scoparia and the Uma notata complex. Multispecies coalescent analyses with one fossil calibration inferred a Paleogene origin for the total clade of Uma and a Pliocene or Pleistocene divergence between Uma scoparia and the Uma notata complex. The fossil and the total and crown clades of Uma precede the evolution of modern desert ecosystems in the southwestern United States and northern Mexico by millions of years.ConclusionsThe total clade and the crown clade of Uma were not restricted to arid deserts throughout their evolutionary histories. I demonstrate that an apomorphy-based diagnosis can be used to identify fossils of isolated skeletal elements for at least one clade of phrynosomatid lizard, and suggest exercising caution when using environmental tolerances of extant taxa to hypothesize paleoecological reconstructions.

Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats

In wheatears and related species (‘open-habitat chats’), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species’ relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats’ plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1’300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.

Parallel plumage colour evolution and introgressive hybridization in wheatears.

Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa-pied wheatear (O.pleschanka), Cyprus wheatear (Oenanthe cypriaca), and western and eastern subspecies of black-eared wheatear (O.h.hispanica and O.h.melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20,000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.

Molecular phylogenetics and species-level systematics of Baylisascaris.

Nucleotide sequences representing nine genes and five presumptive genetic loci were used to infer phylogenetic relationships among seven Baylisascaris species, including one species with no previously available molecular data. These genes were used to test the species status of B. procyonis and B. columnaris using a coalescent approach. Phylogenetic analysis based on combined analysis of sequence data strongly supported monophyly of the genus and separated the species into two main clades. Clade 1 included B. procyonis, B. columnaris, and B. devosi, species hosted by musteloid carnivores. Clade 2 included B. transfuga and B. schroederi from ursids, B. ailuri, a species from the red panda (a musteloid), and B. tasmaniensis from a marsupial. Within clade 2, geographic isolates of B. transfuga, B. schroederi (from giant panda), and B. ailuri formed a strongly supported clade. In certain analyses (e.g., some single genes), B. tasmaniensis was sister to all other Baylisascaris species rather than sister to the species from ursids and red panda. Using one combination of priors corresponding to moderate population size and shallow genetic divergence, the multispecies coalescent analysis of B. procyonis and B. columnaris yielded moderate support (posterior probability 0.91) for these taxa as separate species. However, other prior combinations yielded weak or no support for delimiting these taxa as separate species. Similarly, tree topologies constrained to represent reciprocal monophyly of B. columnaris and B. procyonis individuals (topologies consistent with separate species) were significantly worse in some cases, but not others, depending on the dataset analyzed. An expanded analysis of SNPs and other genetic markers that were previously suggested to distinguish between individuals of B. procyonis and B. columnaris was made by characterization of additional individual nematodes. The results suggest that many of these SNPs do not represent fixed differences between nematodes derived from raccoon and skunk hosts.

Cryptic diversity, pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris

The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp. G, and C. zebrina were also identified in association with CLS on B. vulgaris. Cercospora apii and C. cf. flagellaris were pathogenic to table beet but Cercospora sp. G and C. zebrina did not cause disease. Genealogical concordance phylogenetic species recognition, GMYC and PTP methods failed to differentiate C. apii and C. beticola as separate species. On the other hand, multi-species coalescent analysis based on BFD supported separation of C. apii and C. beticola into distinct species; and provided evidence of evolutionary independent lineages within C. beticola. Extensive intra- and intergenic recombination, incomplete lineage sorting and dominance of clonal reproduction complicate evolutionary species recognition in the genus Cercospora. The results warrant morphological and phylogenetic studies to disentangle cryptic speciation within C. beticola.

Species tree phylogeny, character evolution, and biogeography of the Patagonian genus Anarthrophyllum Benth. (Fabaceae)

Geologic events promoting the aridization of southern South America contributed to lineage divergences and species differentiation through geographic (allopatric divergence) and biotic and abiotic factors (ecological divergence). For the genus Anarthrophyllum, which is distributed in arid and semi-arid regions of Patagonia, we assessed how these factors affected species diversification and reconstructed its possible biogeographic history in South American arid environments. Sequences were obtained from two molecular markers: the ITS nuclear region and the trnS-trnG plastid region. Using Parsimony, Maximum likelihood and Bayesian inference individual gene trees were reconstructed, and a species tree was obtained using multi-species coalescent analysis. Divergence times among species were estimated using secondary calibrations. Flexible Bayesian models and stochastic character mapping were used to elucidate ancestral geographic distributions and the evolution of the floral and vegetative phenotypes in the genus. Gene trees and species tree analyses strongly support Anarthrophyllum as monophyletic; all analyses consistently retrieved three well-supported main clades: High Andean Clade, Patagonian Clade 1, and Patagonian Clade 2. Main diversification events occurred concomitant with the Andean uplift and steppe aridization; the Andean mountain range possibly acted as a species barrier for the High Andean Clade. Vegetative traits showed adaptations to harsh climates in some clades, while pollinator-related floral features were associated with independent diversification in bee- and bird-pollinated clades within both Patagonian Clades. In conclusion, evolutionary and biogeographic history of Anarthrophyllum resulted from the action of ecological, historical, and geographic factors that acted either alternatively or simultaneously.

Impact of long-term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages.

Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.

The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation.

Our recent estimation of the divergence time and isolation of Death Valley pupfishes, including the iconic Devil's Hole pupfish (DHP), rewrote widespread assumptions about this group. These species were previously assumed to be relic populations isolated over millions of years; our genomic analyses indicated recent colonization of Devil's Hole within the past 105–830 years and frequent gene flow among Death Valley populations [1]. These results understandably attracted substantial attention given the iconic battle for conservation and intense management of DHP [2]; nonetheless, a young age for this species should not diminish its conservation value. Indeed, we argue that the unique natural history of this species makes it a prime candidate for exhibiting one of the fastest mutation rates observed in any vertebrate [3]. Saglam et al . [4] argue that we overestimated the substitution rate, the rate at which mutations occur and fix between lineages over time, in pupfishes due to our analysis of a concatenated dataset of RADseq loci and therefore underestimated the age of DHP. Specifically, Saglam et al . argue that a multi-species coalescent analysis would remove our bias and provide strikingly different results. Here, we test this assumption by reanalysing our original RADseq dataset under a multi-species coalescent model and comparing the estimated substitution rates to an analysis of concatenated RADseq loci. It is well known that divergence times estimated from concatenated, multi-gene analyses can overestimate species divergence times due to older gene-tree divergence compared with the true species-tree divergence time, a fact that we both cited [5] and demonstrated in our study: our concatenated gene analysis estimated DHP divergence at 2500–6500 years (fig. 2 of [1]) versus our coalescent analysis using dadi [6 …

Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined.

Kozak etal. (2015, Syst. Biol., 64: 505) portrayed the inference of evolutionary history among Heliconius and allied butterfly genera as a particularly difficult problem for systematics due to prevalent gene conflict caused by interspecific reticulation. To control for this, Kozak etal. conducted a series of multispecies coalescent phylogenetic analyses that they claimed revealed pervasive conflict among markers, but ultimately chose as their preferred hypothesis a phylogenetic tree generated by the traditional supermatrix approach. Intrigued by this seemingly contradictory set of conclusions, we conducted further analyses focusing on two prevalent aspects of the data set: missing data and the uneven contribution of phylogenetic signal among markers. Here, we demonstrate that Kozak etal. overstated their findings of reticulation and that evidence of gene-tree conflict is largely lacking. The distribution of intrinsic homoplasy and incongruence homoplasy in their data set does not follow the pattern expected if phylogenetic history had been obscured by pervasive horizontal gene flow; in fact, noise within individual gene partitions is ten times higher than the incongruence among gene partitions. We show that the patterns explained by Kozak etal. as a result of reticulation can be accounted for by missing data and homoplasy. We also find that although the preferred topology is resilient to missing data, measures of support are sensitive to, and strongly eroded by too many empty cells in the data matrix. Perhaps more importantly, we show that when some taxa are missing almost all characters, adding more genes to the data set provides little or no increase in support for the tree.

Biogeographical evidence for common vicariance and rare dispersal in a southern Appalachian harvestman (Sabaconidae, Sabacon cavicolens)

AbstractAimSpecies or higher taxa that are obviously dispersal‐limited, but which occupy large geographical distributions, represent a biogeographical paradox. Dispersal must have happened, likely under special and infrequent environmental conditions, but details have been lost to history. The overarching goal of our research is to understand the details of a ‘common vicariance, rare dispersal’ biogeographical history in a widespread but habitat‐specialized harvestman species (Sabacon cavicolens) with a southern Appalachian centre of distribution.LocationEastern North America, southern Appalachians.MethodsWe assessed cryptic speciation using mitochondrial and nuclear gene DNA sequence data, testing alternative delimitation hypotheses using multispecies coalescent analyses. We also tested whether riverine barriers are associated with mitochondrial genealogical structuring, focusing on multiple rivers in the southern Blue Ridge physiographical province. Finally, we conducted population genetic analyses to assess female‐based range expansion out of the southern Blue Ridge.ResultsGenetic analyses suggest a large number of species‐level lineages within S. cavicolens, although we prefer a more conservative three‐species hypothesis. These putative species are geographically cohesive and allopatric (Ozarks, Cumberland Plateau, southern Blue Ridge), with the Blue Ridge species including multiple divergent mitochondrial haplogroups. Several genealogical breaks in the Blue Ridge species coincide with riverine barriers, separating mostly allopatric mitochondrial lineages. Contrasting with evidence for constrained gene flow and vicariance, two Blue Ridge haplogroups reveal extensive range expansion both northwards and westwards, resulting in the widespread distribution of closely related haplotypes, and occasional sympatry of dispersive haplotypes.Main ConclusionsHidden beneath the apparently widespread distribution of a single species is a history of old vicariance separating geographically disjunct cryptic species. How these lineages came to occupy such disparate geographies is illustrated by dynamics within the Blue Ridge species, where both in situ vicariance and long‐distance dispersal have shaped a ‘common vicariance, rare dispersal’ biogeographical history.

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

Species delimitation in trematodes using DNA sequences: Middle-American Clinostomum as a case study.

The recent development of genetic methods allows the delineation of species boundaries, especially in organisms where morphological characters are not reliable to differentiate species. However, few empirical studies have used these tools to delineate species among parasitic metazoans. Here we investigate the species boundaries of Clinostomum, a cosmopolitan trematode genus with complex life cycle. We sequenced a mitochondrial [cytochrome c oxidase subunit I (COI)] gene for multiple individuals (adults and metacercariae) from Middle-America. Bayesian phylogenetic analysis of the COI uncovered five reciprocally monophyletic clades. COI sequences were then explored using the Automatic Barcode Gap Discovery to identify putative species; this species delimitation method recognized six species. A subsample was sequenced for a nuclear gene (ITS1, 5·8S, ITS2), and a concatenated phylogenetic analysis was performed through Bayesian inference. The species delimitation of Middle-American Clinostomum was finally validated using a multispecies coalescent analysis (species tree). In total, five putative species are recognized among our samples. Mapping the second intermediate hosts (fish) onto the species tree suggests that metacercariae of these five species exhibit some level of host specificity towards their fish intermediate host (at the family level), irrespective of geographical distribution.

Cleistogamy and phylogenetic position ofViola uliginosa(Violaceae) re-examined

Viola uliginosa is an endangered species throughout its range in Central Europe. Based on an unusual combination of morphological characters, including a reported lack of cleistogamous (CL) flowers, it was previously placed in the monotypic subsection Repentes, section Viola. Available individual phylogenetic analyses identify V. uliginosa as a lineage deeply embedded in section Viola, but hitherto its exact position was unknown. Here we confirm the occurrence of cleistogamy in V. uliginosa. Unlike other species of section Viola, V. uliginosa produced both chasmogamous and CL flowers at the same time, not at different times of the year (seasonal cleistogamy). The two flower types differed conspicuously in morphology and microstructure, especially in size and shape of the pistil and stamens as confirmed by scanning electron microscopy. Secondly, we resolved the phylogenetic position of V. uliginosa as a lineage deeply embedded in subsection Rostratae by means of a multigene multispecies coalescent analysis using *BEAST. In this analysis, V. mirabilis and V. uliginosa were successive sisters to the rest of subsection Rostratae and, because allopolyploids exist between V. mirabilis and the last one, subsection Rostratae needs to comprise all these taxa to be monophyletic. The evolution of key morphological traits is briefly discussed.

Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider.

Mediterranean mountain ranges harbour highly endemic biota in islandlike habitats. Their topographic diversity offered the opportunity for mountain species to persist in refugial areas during episodes of major climatic change. We investigate the role of Quaternary climatic oscillations in shaping the demographic history and distribution ranges in the spider Harpactocrates ravastellus, endemic to the Pyrenees. Gene trees and multispecies coalescent analyses on mitochondrial and nuclear DNA sequences unveiled two distinct lineages with a hybrid zone around the northwestern area of the Catalan Pyrenees. The lineages were further supported by morphological differences. Climatic niche-based species distribution models (SDMs) identified two lowland refugia at the western and eastern extremes of the mountain range, which would suggest secondary contact following postglacial expansion of populations from both refugia. Neutrality test and approximate Bayesian computation (ABC) analyses indicated that several local populations underwent severe bottlenecks followed by population expansions, which in combination with the deep population differentiation provided evidence for population survival during glacial periods in microrefugia across the mountain range, in addition to the main Atlantic and Mediterranean (western and eastern) refugia. This study sheds light on the complexities of Quaternary climatic oscillations in building up genetic diversity and local endemicity in the southern Europe mountain ranges.

Patterns of phylogenetic incongruence in Medicago found among six loci

The species phylogeny of Medicago L. (Leguminosae) remains unresolved, as there is significant incongruence between the published gene phylogenies. Here, we compare six of these gene phylogenies of Medicago, inferred from unlinked loci from the nuclear, chloroplast and mitochondrial genomes. Data from all loci were re-analysed, including gap-coding of initial data sets, and dated phylogenies were produced. The patterns of species relationships observed in the six dated phylogenies are compatible with several different biological processes, such as incomplete lineage sorting and hybridisation. A subset of the original sampling that included 29 taxa was also analysed using coalescent-based tree distance comparisons. The observed topological distances suggest that differences between gene phylogenies cannot be solely attributed to incomplete lineage sorting. Hybridisation is strongly suspected to have occurred in the history of many taxa in the genus, because of overlapping divergence times between suspected hybrids and each parental lineage, confirming earlier results based on only two genes. An attempt to reconcile the conflicting histories in a multispecies coalescent analysis, using multiple labels for taxa with hybrid histories, did not produce satisfactory results and may be fatally limited. We conclude that although the currently available data are not sufficient to clarify relationships in Medicago, many cases of hybridisation are probable. The phylogenetic history of the genus is therefore better understood as a network and not a single tree. This raises concerns over previous studies that have used single gene trees as summaries of the history of species relationships.

Unexpected species diversity and contrasting evolutionary hypotheses in Hebeloma (Agaricales) sections Sinapizantia and Velutipes in Europe

Hebeloma velutipes is one of the most common and abundant members of the ectomycorrhizal basidiomycete genus and H. sinapizans is one of its oldest and most commonly recorded species. Using large sample sizes, several loci and the analysis of types, we explored the taxonomy, species limits, distribution and the infrageneric classification of these two species and their relatives. By relying almost exclusively on sequenced material, we were able to attain a marked refinement of species descriptions. Phylogenetic results are congruent with respect to the delimitation of species, but suggest conflicting evolutionary histories of the species phylogeny. Using multi-species coalescent analysis, phylogenetic support for H. sects. Velutipes and Sinapizantia was assessed, finding clear support for H. sect. Sinapizantia but ambiguous results for H. sect. Velutipes. One species, H. subconcolor, previously accommodated in H. sect. Denudata, is placed in H. sect. Velutipes. Hebeloma bulbiferum, so far not considered in systematic treatments, is shown to belong to H. sect. Sinapizantia. Unexpectedly, H. velutipes turned out to be distinct from H. leucosarx. Hebeloma erebium comb. nov., H. celatum sp. nov. and H. quercetorum, formerly treated as a single species (H. quercetorum), are demonstrated to be three taxa that are clearly distinct in molecular terms, even though, morphologically, they can be deceptively similar; H. erebium and H. quercetorum are, moreover, geographically distinct. The morphological characters used to distinguish the ten recognised European species are outlined. Finally, a lectotype and an epitype are designated for H. sinapizans and a lectotype for H. quercetorum.

Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia.

Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M.montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic-scale data sets are gathered for taxa found in naturally fragmented habitats.

Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict.

Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The evolution of NP has been intensively investigated in the last decade by studies focusing on their phylogeny and timescale. However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene trees within the proposed phylogenies. We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids. The molecular phylogeny of NP has been difficult to solve because of population-level phenomena at the early evolution of the lineage. The association of evolutionary variation with the distribution of gene trees within proposed phylogenies is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time. This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms.

Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study

Many single-species freshwater phylogeographic studies have been carried out in south-east Queensland; however comparative phylogeography requires multiple lines of evidence to infer deep, significant relationships between landscape and biota. The present study aimed to test conclusions resulting from single taxon studies in a multispecies comparative framework: (1) how influential are river basins in the genetic structure of freshwater species; (2) are there biogeographic frontiers between groups of basins; and (3) could deep intraspecific lineages be explained by a single event? New and existing data from 33 freshwater species (23 fishes and 10 crustaceans) were combined, and both standard single-species analyses (haplotype networks, genetic distances, ΦST) and multispecies methods (hierarchical ABC) were carried out for 1814 sequences from eight basins. More than half of the species displayed a high phylogeographic structure and contained at least two distinct lineages. Almost all of the lineage divergences displayed an element of north/south geographic breaks, with the most influential boundary being between the Mary and Brisbane rivers. Of the 11 basin-pair multispecies coalescent analyses, four implied a single divergence as being most likely. A regional analysis of deep lineages within 16 taxon-pairs resulted in a strongly supported inference of a single divergence, probably dating to the Pleistocene. Basin boundaries are a key determinant of phylogeographic patterns for most of these freshwater species, although the specific biogeographic relationship between basins often varies depending on the species. There are a number of influential biogeographic frontiers, with the Brisbane-Mary being the most important. The finding that a single event may be responsible for multiple deep lineages across the region implies that a highly influential climate change event may have been detected. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 554–569.

Molecular phylogeny of the genusMargotrema(Digenea: Allocreadiidae), parasitic flatworms of goodeid freshwater fishes across central Mexico: species boundaries, host-specificity, and geographical congruence

We explored the genetic variation at the intraspecific level of two putative species of Margotrema, M. bravoae and M. guillerminae, to establish the species boundaries. Sequences of a mitochondrial (COI) and nuclear (ITS1) gene were obtained for 125 specimens distributed in 15 localities from seven hydrological systems. An alignment of 750 and 831 bp including gaps of COI and ITS1, respectively, was assembled. We analysed the gene fragments separately as well as together by using Bayesian inference for phylogenetic reconstruction. Based on the phylogenetic analyses, an ultrametric tree was built for each gene, and a general mixed Yule-coalescent model for species delimitation was carried out. A multispecies coalescent analysis was performed in *BEAST using both molecular markers. The results show four independent evolutionary lineages that we interpret as two valid species of Margotrema; the first is represented by an independent lineage, and the second is composed of three lineages. Because the species M. bravoae and M. guillerminae nested together within these three lineages, the validity of M. guillerminae as an independent species is questioned, and it is proposed to represent a junior synonym of M. bravoae. Each lineage shows a congruent geographical pattern with respect to the hydrological system where they occur. Additionally, each lineage shows congruence with respect to the hosts they parasitize, either at the species or at higher taxonomical levels (tribe). The parasite evolutionary history is congruent with the evolutionary and biogeographical history of their hosts. © 2013 The Linnean Society of London