Bioregion heterogeneity correlates with extensive mitochondrial DNA diversity in the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae) from southern Africa - evidence for a species complex

<p>Abstract</p> <p>Background</p> <p>Intraspecific variation within the diverse southern African murine rodents has not been extensively investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, <it>Micaelamys namaquensis </it>Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species with four subspecies is recognised, but in the past up to 16 subspecies were described. Thus, this species is a good candidate for the investigation of patterns and processes of diversification in a diverse but under-studied mammalian subfamily and geographic region. Here, we report genetic differentiation based on mitochondrial DNA (mtDNA) cytochrome <it>b </it>(cyt <it>b</it>) sequences among samples collected over an extensive coverage of the species' range.</p> <p>Results</p> <p>Cytochrome <it>b </it>sequences of 360 widely sampled individuals identified 137 unique maternal alleles. Gene tree and phylogeographic analyses of these alleles suggest the presence of at least eight lineages or haplogroups (A-H), with varying degrees of intra-lineage diversity. This differentiation is in contrast with the most recent taxonomic treatment based on cranial morphometrics which only recognised four subspecies. The mtDNA diversity strongly supports earlier views that this taxon may represent a species complex. We further show statistical support for the association of several of these lineages with particular vegetation biomes of southern Africa. The time to the most recent common ancestor (TMRCA) dates to the Pliocene (~5 Mya) whereas coalescent-based divergence time estimates between lineages vary between 813 Kya [0.22 - 1.36] and 4.06 Mya [1.21 - 4.47]. The major diversification within lineages occurred during the Pleistocene. The identification of several regions of sympatry of distinct lineages offers future opportunities for the elucidation of the underlying speciation processes in the suggested species complex.</p> <p>Conclusions</p> <p>Similar to other African murine rodents, <it>M. namaquensis </it>radiated during the Pliocene and Pleistocene coinciding with major periods of aridification and the expansion of savanna habitats. The suggested species complex is represented by at least eight lineages of which the majority are confined to only one or a few neighbouring biomes/bioregions. Contrasting intra-lineage phylogeographic patterns suggest differences in adaptation and responses to Plio-Pleistocene climatic and vegetation changes. The role of ecological factors in driving speciation in the group needs further investigation.</p

Odour dialects among wild mammals

Across multiple taxa, population structure and dynamics depend on effective signalling between individuals. Among mammals, chemical communication is arguably the most important sense, underpinning mate choice, parental care, territoriality and even disease transmission. There is a growing body of evidence that odours signal genetic information that may confer considerable benefits including inbreeding avoidance and nepotism. To date, however, there has been no clear evidence that odours encode population-level information in wild mammals. Here we demonstrate for the first time the existence of ‘odour dialects’ in genetically distinct mammalian subpopulations across a large geographical scale. We found that otters, Lutra lutra, from across the United Kingdom possess sex and biogeography-specific odours. Subpopulations with the most distinctive odour profiles are also the most genetically diverse but not the most genetically differentiated. Furthermore, geographic distance between individuals does not explain regional odour differences, refuting other potential explanations such as group odour sharing behaviour. Differences in the language of odours between subpopulations have the potential to affect individual interactions, which could impact reproduction and gene-flow

Dispersal and genetic structures in a tropical small mammal, the Bornean tree shrew (Tupaia longipes), in a fragmented landscape along the Kinabatangan River, Sabah, Malaysia

Background Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals. To fill this gap in knowledge, we used nuclear and mitochondrial DNA markers to assess genetic diversity, gene flow and the genetic structure in the Bornean tree shrew, Tupaia longipes, that inhabits forest fragments of the Lower Kinabatangan Wildlife Sanctuary, Sabah. Furthermore, we used these markers to assess dispersal regimes in male and female T. longipes. Results In addition to the Kinabatangan River, a known barrier for dispersal in tree shrews, the heterogeneous landscape along the riverbanks affected the genetic structure in this species. Specifically, while in larger connected forest fragments along the northern riverbank genetic connectivity was relatively undisturbed, patterns of genetic differentiation and the distribution of mitochondrial haplotypes in a local scale indicated reduced migration on the strongly fragmented southern riverside. Especially, oil palm plantations seem to negatively affect dispersal in T. longipes. Clear sex-biased dispersal was not detected based on relatedness, assignment tests, and haplotype diversity. Conclusion This study revealed the importance of landscape connectivity to maintain migration and gene flow between fragmented populations, and to ensure the long-term persistence of species in anthropogenically disturbed landscapes

Genomic selection strategies for breeding adaptation and production in dairy cattle under climate change

Livestock production both contributes to and is affected by global climate change, and substantial modifications will be required to increase its climate resilience. In this context, reliance on dominant commercial livestock breeds, featuring small effective population sizes, makes current production strategies vulnerable if their production is restricted to environments, which may be too costly to support under future climate scenarios. The adaptability of animal populations to future environments will therefore become important. To help evaluate the role of genetics in climate adaptation, we compared selection strategies in dairy cattle using breeding simulations, where genomic selection was used on two negatively correlated traits for production (assumed to be moderately heritable) and adaptation (assumed to have low heritability). Compared with within-population breeding, genomic introgression produced a more positive genetic change for both production and adaptation traits. Genomic introgression from highly adapted but low production value populations into highly productive but low adaptation populations was most successful when the adaptation trait was given a lower selection weight than the production trait. Genomic introgression from highly productive population to highly adapted population was most successful when the adaptation trait was given a higher selection weight than the production trait. Both these genomic introgression schemes had the lowest risk of inbreeding. Our results suggest that both adaptation and production can potentially be improved simultaneously by genomic introgression

The contribution of digital sequence information to conservation biology: a Southern African perspective

Many recent contributions have made a compelling case that genetic diversity is not adequately reflected in international frameworks and policies, as well as in local governmental processes implementing such frameworks. Using digital sequence information (DSI) and other publicly available data is supported to assess genetic diversity, toward formulation of practical actions for long‐term conservation of biodiversity, with the particular goal of maintaining ecological and evolutionary processes. Given the inclusion of specific goals and targets regarding DSI in the latest draft of the Global Biodiversity Framework negotiated at the 15th Conference of the Parties (COP15) in Montreal in December 2022 and the crucial decisions on access and benefit sharing to DSI that will be taken in the coming months and future COP meetings, a southern African perspective on how and why open access to DSI is essential for the conservation of intraspecific biodiversity (genetic diversity and structure) across country borders is provided

Inferring fine-scale spatial structure of the brown bear (Ursus arctos) population in the Carpathians prior to infrastructure development

Landscape genetics is increasingly being used in landscape planning for biodiversity conservation by assessing habitat connectivity and identifying landscape barriers, using intraspecific genetic data and quantification of landscape heterogeneity to statistically test the link between genetic variation and landscape variability. In this study we used genetic data to understand how landscape features and environmental factors influence demographic connectedness in Europe’s largest brown bear population and to assist in mitigating planned infrastructure development in Romania. Model-based clustering inferred one large and continuous bear population across the Carpathians suggesting that suitable bear habitat has not become sufficiently fragmented to restrict movement of individuals. However, at a finer scale, large rivers, often located alongside large roads with heavy traffic, were found to restrict gene flow significantly, while eastern facing slopes promoted genetic exchange. Since the proposed highway infrastructure development threatens to fragment regions of the Carpathians where brown bears occur, we develop a decision support tool based on models that assess the landscape configuration needed for brown bear conservation using wildlife corridor parameters. Critical brown bear corridors were identified through spatial mapping and connectivity models, which may be negatively influenced by infrastructure development and which therefore require mitigation. We recommend that current and proposed infrastructure developments incorporate these findings into their design and where possible avoid construction measures that may further fragment Romania’s brown bear population or include mitigation measures where alternative routes are not feasible

Genetic diversity and cryptic population re-establishment: management implications for the Bojer's skink (Gongylomorphus bojerii)

Understanding genetic structure and diversity underpins the management of isolated populations. Small populations confined to islands may require effective genetic management for population persistence due to inbreeding and reduced genetic diversity. Endemic to the offshore islands of mainland Mauritius, the Bojer’s skink (Gongylomorphus bojerii) has previously been managed as two genetic units due to divergence between populations to the north and south-east. In 2009, a few individuals were discovered on the south-eastern island Ile de la Passe (IDLP), an island within its former range where the species was believed to have gone extinct. This island was later supplemented with translocations from other south-eastern islands, but individual geographic origin and the genetic consequences of these translocations remains unknown. Demographic population history and translocation events were reconstructed using a suite of microsatellite markers and the mitochondrial DNA cytochrome b gene, assessing two northern and three south-eastern populations to infer the geographic origin of the IDLP individuals, and to assess the population’s genetic diversity and structure. Although IDLP showed significant differentiation from all other populations, all analyses indicated a south-eastern origin, possibly founded by a single gravid female. Subsequent translocations have so far failed to ameliorate IDLP’s genetic diversity. In addition, admixture analysis was used to track translocation and gene-flow in IDLP. We recommend using additional translocations from other south-eastern islands to further genetically support IDLP. Our study highlights the need to clarify cryptic population structure and utilise post-translocation genetic monitoring among similarly managed populations, particularly endangered island populations

Species separation within, and preliminary phylogeny for, the leafhopper genus Anoscopus with particular reference to the putative British endemic Anoscopus duffieldi (Hemiptera: Cicadellidae)

The subfamily Aphrodinae (Hemiptera: Cicadellidae) contains ~33 species in Europe within four genera. Species in two genera in particular, Aphrodes and Anoscopus, have proved to be difficult to distinguish morphologically. Our aim was to determine the status of the putative species Anoscopus duffieldi, found only on the RSPB Nature Reserve at Dungeness, Kent, a possible rare UK endemic. DNA from samples of all seven UK Anoscopus species (plus Anoscopusalpinus from the Czech Republic) were sequenced using parts of the mitochondrial cytochrome oxidase I and 16S rRNA genes. Bayesian inference phylogenies were created. Specimens of each species clustered into monophyletic groups, except for Anoscopusalbifrons, A. duffieldi and Anoscopuslimicola. Two A. albifrons specimens grouped with A. duffieldi repeatedly with strong support, and the remaining A. albifrons clustered within A. limicola. Genetic distances suggest that A. albifrons and A. limicola are a single interbreeding population (0% divergence), while A. albifrons and A. duffieldi diverged by only 0.28%. Shared haplotypes between A. albifrons, A. limicola and A. duffieldi strongly suggest interbreeding, although misidentification may also explain these topologies. However, all A. duffieldi clustered together in the trees. A conservative approach might be to treat A. duffieldi, until other evidence is forthcoming, as a possible endemic subspecies

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results