Fine-scale morphological, genomic, reproductive, and symbiont differences delimit the Caribbean octocorals Plexaura homomalla and P. kükenthali

Octocorals are conspicuous members of coral reefs and deep-sea ecosystems. Yet, species boundaries and taxonomic relationships within this group remain poorly understood, hindering our understanding of this essential component of the marine fauna. We used a multifaceted approach to revisit the systematics of the Caribbean octocorals Plexaura homomalla and Plexaura kükenthali, two taxa that have a long history of taxonomic revisions. We integrated morphological and reproductive analyses with high-throughput sequencing technology to clarify the relationship between these common gorgonians. Although size and shape of the sclerites are significantly different, there is overlap in the distributions making identification based on sclerites alone difficult. Differences in reproductive timing and mode of larval development were detected, suggesting possible mechanisms of pre-zygotic isolation. Furthermore, there are substantial genetic differences and clear separation of the two species in nuclear introns and single-nucleotide polymorphisms obtained from de novo assembled transcriptomes. Despite these differences, analyses with SNPs suggest that hybridization is still possible between the two groups. The two nascent species also differed in their symbiont communities (genus Breviolum) across multiple sampling sites in the Caribbean. Despite a complicated history of taxonomic revisions, our results support the differentiation of P. homomalla and P. kükenthali, emphasizing that integrative approaches are essential for Anthozoan systematics.

Evidence of differential genetic introgression at multiple localities between Neotoma floridana and N. micropus

To determine the extent of genetic introgression along the parapatric border between Neotoma floridana and N. micropus, 140 woodrats were sampled from 21 localities in Kansas, Oklahoma, and Texas, at varying distances from the proposed species boundaries. All individuals were examined at the mitochondrial cytochrome-b gene (Cytb) and two nuclear introns: intron seven of the Beta fibrinogen gene (Fgb-I7) and intron 2 of the vertebrate alcohol dehydrogenase gene (Adh1-I2). Additionally, individuals from a putative contact zone were genotyped using six microsatellite loci to better analyze population structure. Evidence of mixed ancestry was detected in 55 of 140 (39 %) individuals, at 10 of 21 (48 %) localities up to ~150 km from the proposed parapatric boundary. A pattern of differential admixture detected between the two nuclear markers suggested variation in selection pressures at the Adh1-I2 and Fgb-I7 markers is dependent upon the genomic makeup of the individual. Together, the mitochondrial and nuclear markers indicate evidence of historical hybridization and suggest that hybrid zones within this system are transient in nature.

Comprehensive evidence for subspecies designations in Cook’s Petrel Pterodroma cookii with implications for conservation management

Summary Cook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.

Genetic, morphological and acoustic differentiation of African trident bats (Rhinonycteridae: Triaenops)

Rhinonycteridae (trident bats) are a small Palaeotropical family of insectivorous bats allied to Hipposideridae. Their taxonomy has been in a state of flux. Here, we use mitochondrial and nuclear sequences to evaluate species relationships, confirming the monophyly of both Triaenops and Paratriaenops. Although most Triaenops afer specimens are recovered as a group, mitochondrial analyses strongly support some Kenyan individuals as members of Triaenops persicus. Analyses of four nuclear introns (ACOX2, COPS7A, RODGI and STAT5A) strongly support the mitochondrial topology. Morphometric analysis of the skull, external morphology and echolocation calls confirm that the Triaenops from the Rift Valley in Kenya (Nakuru, Baringo and Pokot counties) are distinct from typical T. afer in coastal (Kilifi and Kwale counties) or interior (Laikipia and Makueni counties) colonies. We interpret these analyses to indicate that two species of Triaenops occur in East Africa: T. afer in coastal regions along the Indian Ocean and in the highlands of central Kenya and Ethiopia, and T. persicus in the Rift Valley of Kenya. Although they appear widely disjunct from Middle Eastern populations, Kenyan T. persicus might be more widely distributed in the Rift Valley; they are somewhat differentiated from Middle Eastern populations in terms of both cranial morphology and vocalizations.

Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae)

The Old World leaf-nosed bats (Hipposideridae) are aerial and gleaning insectivores that occur throughout the Paleotropics. Both their taxonomic and phylogenetic histories are confused. Until recently, the family included genera now allocated to the Rhinonycteridae and was recognized as a subfamily of Rhinolophidae. Evidence that Hipposideridae diverged from both Rhinolophidae and Rhinonycteridae in the Eocene confirmed their family rank, but their intrafamilial relationships remain poorly resolved. We examined genetic variation in the Afrotropical hipposiderids Doryrhina, Hipposideros, and Macronycteris using relatively dense taxon-sampling throughout East Africa and neighboring regions. Variation in both mitochondrial (cyt-b) and four nuclear intron sequences (ACOX2, COPS, ROGDI, STAT5) were analyzed using both maximum likelihood and Bayesian inference methods. We used intron sequences and the lineage delimitation method BPP—a multilocus, multi-species coalescent approach—on supported mitochondrial clades to identify those acting as independent evolutionary lineages. The program StarBEAST was used on the intron sequences to produce a species tree of the sampled Afrotropical hipposiderids. All genetic analyses strongly support generic monophyly, with Doryrhina and Macronycteris as Afrotropical sister genera distinct from a Paleotropical Hipposideros; mitochondrial analyses interpose the genera Aselliscus, Coelops, and Asellia between these clades. Mitochondrial analyses also suggest at least two separate colonizations of Africa by Asian groups of Hipposideros, but the actual number and direction of faunal interchanges will hinge on placement of the unsampled African-Arabian species H. megalotis. Mitochondrial sequences further identify a large number of geographically structured clades within species of all three genera. However, in sharp contrast to this pattern, the four nuclear introns fail to distinguish many of these groups and their geographic structuring disappears. Various distinctive mitochondrial clades are consolidated in the intron-based gene trees and delimitation analyses, calling into question their evolutionary independence or else indicating their very recent divergence. At the same time, there is now compelling genetic evidence in both mitochondrial and nuclear sequences for several additional unnamed species among the Afrotropical Hipposideros. Conflicting appraisals of differentiation among the Afrotropical hipposiderids based on mitochondrial and nuclear loci must be adjudicated by large-scale integrative analyses of echolocation calls, quantitative morphology, and geometric morphometrics. Integrative analyses will also help to resolve the challenging taxonomic issues posed by the diversification of the many lineages associated with H. caffer and H. ruber.

Strong population structure and limited gene flow between Yellow-billed Ducks and Mallards in southern Africa

Secondary contact and hybridization between recently diverged taxa have been increasing due to anthropogenic changes to the environment. Determining whether secondary contact leads to gene flow between species is important for understanding both the evolutionary consequences of such events (i.e. genetic swamping, speciation reversal, hybrid speciation) and for establishing proper conservation measures. Mallards (Anas platyrhynchos), which natively have a Holarctic distribution, have been introduced nearly worldwide due to game-farm and domestic pet releases. Their expanding range has resulted in secondary contact and increased incidences of hybridization with many closely related Mallard-like ducks that comprise the Mallard complex. Here, we assay molecular diversity for 19 nuclear introns and the mitochondrial DNA for wild Mallards (n = 50) across their Holarctic range and Yellow-billed Ducks (n = 30–75; Anas undulata) from southern Africa to determine population genetic structure and test for evidence of Mallard introgression into Yellow-billed Ducks. While we found limited support for contemporary gene flow across nuclear markers, we provide evidence from mitochondrial DNA that best supports ancient gene flow between Yellow-billed Ducks and Mallards. Yellow-billed Ducks best fit a single population at nuclear markers but show some location-specific mtDNA structure that suggests recent founder or bottleneck events. Although we find that introgression from Mallards into Yellow-billed Duck is limited, Yellow-billed Duck populations should be monitored to determine if expanding feral Mallard populations in southern Africa are increasing introgression.

Genetic variation and relationships among Afrotropical species of Myotis (Chiroptera: Vespertilionidae)

The genus Myotis is nearly cosmopolitan and the second-most speciose genus of mammals, but its Afrotropical members are few and poorly known. We analyzed phylogenetic and phylogeographic relationships of six of the eight known Afrotropical species using Cytb and sequences from four nuclear introns. Using Bayesian and maximum-likelihood approaches to generate single-locus, concatenated, and species trees, we confirmed prior evidence that the clade containing Afrotropical Myotis also contains both Palearctic and Indomalayan members. Additionally, we demonstrate that M. bocagii is sister to the Indian Ocean species M. anjouanensis, that this group is sister to M. tricolor and the Palearctic M. emarginatus, and find evidence suggesting that M. welwitschii is the earliest-diverging Afrotropical species and sister to the remainder. Although M. tricolor and M. welwitschii are both currently regarded as monotypic, both mitochondrial and nuclear data sets document significant, largely concordant geographic structure in each. Evidence for the distinction of two lineages within M. tricolor is particularly strong. On the other hand, geographic structure is lacking in M. bocagii, despite the current recognition of two subspecies in that species. Additional geographic sampling (especially at or near type localities), finer-scale sampling (especially in zones of sympatry), and integrative taxonomic assessments will be needed to better document this radiation and refine its nomenclature.

A conservative approach for species delimitation based on multi-locus DNA sequences: a case study of the genus Giraffa (Mammalia, Cetartiodactyla)

Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described.In this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genus Giraffa. Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizes G. camelopardalis sensu strico, G. giraffa, and G. tippelskirchi, is highly supported by phylogenetic analyses and also corroborated by most population genetic and MSC analyses. The three species show high levels of nucleotide divergence in both nuclear (0.35-0.51 %) and mitochondrial sequences (3-4 %), and they are characterised by 7 to 12 exclusive synapomorphies (ES) detected in nine of the 21 nuclear introns analysed for this study. By contrast, other putative species, such as G. peralta, G. reticulata, G. thornicrofti or G. tippelskirchi sensu stricto, do not exhibit any ES in nuclear genes.A robust mito-nuclear conflict was found for the position and monophyly of G. giraffa and G. tippelskirchi, which is explained firstly by a mitochondrial introgression from Masai giraffe to southeastern giraffe during the Pleistocene, and secondly, by gene flow mediated by male dispersal between southern populations (subspecies G.g. giraffa and G.g. angolensis).